PROSITE
Names
More detailed information about this field from each metasource.
PROSITE
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
prosite
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
Names
More detailed information about this field from each metasource.
PROSITE
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
prosite
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
Names
More detailed information about this field from each metasource.
PROSITE
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
prosite
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Description
More detailed information about this field from each metasource.
PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
The PROSITE database (http://www.expasy.org/prosite/) consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that gives useful biological information on the protein family, domain, or functional site identified by the signature.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2021-04-07T11:50:35.288810
Consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
Webpage:
https://prosite.expasy.org/Webpage
More detailed information about this field from each metasource.
https://prosite.expasy.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
http://www.expasy.org/prosite/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2021-04-07T11:50:35.288810
http://prosite.expasy.org
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
Licence:
Name: PROSITE Commercial LicenceLicence name
More detailed information about this field from each metasource.
PROSITE Commercial Licence
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
Licence URL
More detailed information about this field from each metasource.
https://prosite.expasy.org/prosite_license.html
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
Publications:
Publications
More detailed information about this field from each metasource.
New and continuing developments at PROSITE
PMID: 23161676
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
The PROSITE database
PMID: 16381852
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
PMID: 23505298
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
http://dx.doi.org/10.1093/nar/gks1067
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
Publications
More detailed information about this field from each metasource.
New and continuing developments at PROSITE
PMID: 23161676
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
The PROSITE database
PMID: 16381852
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
PMID: 23505298
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
http://dx.doi.org/10.1093/nar/gks1067
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2021-04-07T11:50:35.288810
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New and continuing developments at PROSITE
PubMed citations: 399.
399 articles citing: New and continuing developments at PROSITE
Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide. PMID:33495563
Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice. PMID:33471342
Evolution of A bHLH Interaction Motif. PMID:33466276
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. PMID:33430354
Alternative Splicing Increases Sirtuin Gene Family Diversity and Modulates Their Subcellular Localization and Function. PMID:33418837
Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PMID:33411815
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. PMID:33406800
Bioinformatics: new tools and applications in life science and personalized medicine. PMID:33404829
Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function. PMID:33383823
Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PMID:33362253
Genome-wide identification and evolution of HECT genes in wheat. PMID:33344088
The Central Region of Testican-2 Forms a Compact Core and Promotes Cell Migration. PMID:33321927
Genomic Analysis of Natural Rough Brucella melitensis Rev.1 Vaccine Strains: Identification and Characterization of Mutations in Key Genes Associated with Bacterial LPS Biosynthesis and Virulence. PMID:33302421
Real-time structural motif searching in proteins using an inverted index strategy. PMID:33284792
Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs. PMID:33261041
Characterization of MSlys, the endolysin of Streptococcus pneumoniae phage MS1. PMID:33204659
Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. PMID:33193644
Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases. PMID:33177916
The InterPro protein families and domains database: 20 years on. PMID:33156333
Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines. PMID:33126890
Zinc and Copper Ions Differentially Regulate Prion-Like Phase Separation Dynamics of Pan-Virus Nucleocapsid Biomolecular Condensates. PMID:33081049
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. PMID:33024567
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery. PMID:32946692
Isolation and characterisation of Leishmania donovani protein antigens from urine of visceral leishmaniasis patients. PMID:32925980
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
Hydrogenases and the Role of Molecular Hydrogen in Plants. PMID:32887396
Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. PMID:32823766
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. PMID:32801311
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. PMID:32797185
Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. PMID:32728092
Identification of Sulfenylated Cysteines in Arabidopsis thaliana Proteins Using a Disulfide-Linked Peptide Reporter. PMID:32714340
Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. PMID:32681087
Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. PMID:32655590
A cryptic sequence targets the adhesion complex scaffold ANKS4B to apical microvilli to promote enterocyte brush border assembly. PMID:32636301
Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. PMID:32633465
Genetic factors for short life span associated with evolution of the loss of flight ability. PMID:32607209
Expression of DOCK9 and DOCK11 Analyzed with Commercial Antibodies: Focus on Regulation of Mutually Exclusive First Exon Isoforms. PMID:32605015
Bioinformatics analysis and characterization of a secretory cystatin from Thelohanellus kitauei. PMID:32577834
Putative circumsporozoite protein (CSP) of Plasmodium vivax is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway. PMID:32550551
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PMID:32497121
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
Molecular Characterization of a Date Palm Vascular Highway 1-Interacting Kinase (PdVIK) Under Abiotic Stresses. PMID:32438658
In silico Analyses of Core Proteins and Putative Effector and Immunity Proteins for T6SS in Enterohemorrhagic E. coli. PMID:32432054
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Identification and in silico structural and functional analysis of a trypsin-like protease from shrimp Macrobrachium carcinus. PMID:32351789
A draft genome assembly of spotted hyena, Crocuta crocuta. PMID:32345970
Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. PMID:32327655
RNAseq-Based Prioritization Revealed COL6A5, COL8A1, COL10A1 and MIR146A as Common and Differential Susceptibility Biomarkers for Psoriasis and Psoriatic Arthritis: Confirmation from Genotyping Analysis of 1417 Italian Subjects. PMID:32326527
The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. PMID:32260156
Cauliflower Mosaic Virus TAV, a Plant Virus Protein That Functions like Ribonuclease H1 and is Cytotoxic to Glioma Cells. PMID:32258141
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). PMID:32213914
Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. PMID:32206212
NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases. PMID:32151723
Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa. PMID:32151246
A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage. PMID:32139768
A potential role for integrins in host cell entry by SARS-CoV-2. PMID:32130973
Expression of DOCK10.1 protein revealed with a specific antiserum: insights into regulation of first exon isoforms of DOCK10. PMID:32112301
The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs. PMID:32108236
Cryo-EM structure of the Shigella type III needle complex. PMID:32092125
Molecular and functional insights into a novel teleost malectin from big-belly seahorse Hippocampus abdominalis. PMID:32087279
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis. PMID:31959851
The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection. PMID:31817162
Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta. PMID:31799323
Insights into evolutionary interaction patterns of the 'Phosphorylation Activation Segment' in kinase. PMID:31787816
Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. PMID:31768034
Purification and characterization of proteins in multifloral honey from kelulut bee (stingless bee). PMID:31763485
Overexpression of Saussurea involucrata dehydrin gene SiDHN promotes cold and drought tolerance in transgenic tomato plants. PMID:31738789
Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum. PMID:31731414
NEDD4 family ubiquitin ligases associate with LCMV Z's PPXY domain and are required for virus budding, but not via direct ubiquitination of Z. PMID:31710650
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
Identification and evolution of glucosinolate sulfatases in a specialist flea beetle. PMID:31673017
Condensin II protein dysfunction impacts mitochondrial respiration and mitochondrial oxidative stress responses. PMID:31653782
ExonSkipDB: functional annotation of exon skipping event in human. PMID:31642488
Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers. PMID:31589292
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
The CLN3 gene and protein: What we know. PMID:31568712
Vibrio Proteases for Biomedical Applications: Modulating the Proteolytic Secretome of V. alginolyticus and V. parahaemolyticus for Improved Enzymes Production. PMID:31554228
Differential effects of membrane sphingomyelin and cholesterol on agonist-induced bitter taste receptor T2R14 signaling. PMID:31541354
Role of Clathrin Assembly Protein-2 Beta Subunit during White Spot Syndrome Virus Infection in Black Tiger Shrimp Penaeus monodon. PMID:31530841
Long-chain flavodoxin FldX1 improves Paraburkholderia xenovorans LB400 tolerance to oxidative stress caused by paraquat and H2O2. PMID:31469877
HERCing: Structural and Functional Relevance of the Large HERC Ubiquitin Ligases. PMID:31447701
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
Extreme Diversity of Mycoviruses Present in Isolates of Rhizoctonia solani AG2-2 LP From Zoysia japonica From Brazil. PMID:31355150
The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. PMID:31328227
FunFam protein families improve residue level molecular function prediction. PMID:31319797
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
RNA processing errors triggered by cadmium and integrator complex disruption are signals for environmental stress. PMID:31311534
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
Atopic Eczema: Genetic Analysis of COL6A5, COL8A1, and COL10A1 in Mediterranean Populations. PMID:31275967
In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. PMID:31222109
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PMID:31199787
Protective Function of Novel Fungal Immunomodulatory Proteins Fip-lti1 and Fip-lti2 from Lentinus tigrinus in Concanavalin A-Induced Liver Oxidative Injury. PMID:31198490
In silico Prediction and Validations of Domains Involved in Gossypium hirsutum SnRK1 Protein Interaction With Cotton Leaf Curl Multan Betasatellite Encoded βC1. PMID:31191577
TET2 missense variants in human neoplasia. A proposal of structural and functional classification. PMID:31187595
New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes. PMID:31117933
Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.). PMID:31113386
An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome. PMID:31095560
High precision protein functional site detection using 3D convolutional neural networks. PMID:31051039
Comparative genomics of 10 new Caenorhabditis species. PMID:31007946
Identification and expression analysis of ERECTA family genes in grape (Vitis vinifera L.). PMID:31004330
The potato cyst nematode effector RHA1B is a ubiquitin ligase and uses two distinct mechanisms to suppress plant immune signaling. PMID:30978251
A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions. PMID:30969105
Estimating probabilistic context-free grammars for proteins using contact map constraints. PMID:30918754
Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa. PMID:30890148
Identification of evolutionarily conserved virulence factor by selective pressure analysis of Streptococcus pneumoniae. PMID:30886906
Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway. PMID:30872679
Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PMID:30834181
Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. PMID:30833937
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Moraxella catarrhalis NucM is an entry nuclease involved in extracellular DNA and RNA degradation, cell competence and biofilm scaffolding. PMID:30796312
The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN. PMID:30782655
Cdk8 and Ssn801 Regulate Oxidative Stress Resistance and Virulence in Cryptococcus neoformans. PMID:30755515
Characterization of a phospholipid-regulated β-galactosidase from Akkermansia muciniphila involved in mucin degradation. PMID:30729732
Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species. PMID:30727945
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PMID:30716081
Chromosome conformation capture resolved near complete genome assembly of broomcorn millet. PMID:30683940
PK-profiling method for identifying the expression of resistance-associated genes in partially resistant oats to crown rust. PMID:30594125
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. PMID:30592459
Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. PMID:30576513
Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish. PMID:30545285
Exploring Seipin: From Biochemistry to Bioinformatics Predictions. PMID:30402103
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
A de Novo EDA-Variant in a Litter of Shorthaired Standard Dachshunds with X-Linked Hypohidrotic Ectodermal Dysplasia. PMID:30397018
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. PMID:30385546
Motif-Aware PRALINE: Improving the alignment of motif regions. PMID:30383764
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Global pentapeptide statistics are far away from expected distributions. PMID:30310110
A helical LC3-interacting region mediates the interaction between the retroviral restriction factor Trim5α and mammalian autophagy-related ATG8 proteins. PMID:30282803
Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions. PMID:30248965
Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. PMID:30233522
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. PMID:30210232
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation. PMID:30139304
Tomato MYB49 enhances resistance to Phytophthora infestans and tolerance to water deficit and salt stress. PMID:30132153
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei. PMID:30087354
Cloning and Functional Characterisation of the Duplicated RDL Subunits from the Pea Aphid, Acyrthosiphon pisum. PMID:30065178
MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence. PMID:30011022
A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. PMID:29997638
Learning with multiple pairwise kernels for drug bioactivity prediction. PMID:29949975
DeepFam: deep learning based alignment-free method for protein family modeling and prediction. PMID:29949966
Molecular characterization of a stress-induced NAC gene, GhSNAC3, from Gossypium hirsutum. PMID:29932074
In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51. PMID:29928016
Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression. PMID:29920545
Novel Insights from Comparative In Silico Analysis of Green Microalgal Cellulases. PMID:29914107
SEVENS: a database for comprehensive GPCR genes obtained from genomes: -Update to 68 eukaryotes. PMID:29892516
Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria. PMID:29846396
Evidence for interaction between Hsp90 and the ER membrane complex. PMID:29808299
The conserved RNA recognition motif and C3H1 domain of the Not4 ubiquitin ligase regulate in vivo ligase function. PMID:29802328
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis. PMID:29752410
Patscanui: an intuitive web interface for searching patterns in DNA and protein data. PMID:29722870
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Identification of Placental Aspartic Proteinase in the Eurasian Beaver (Castor fiber L.). PMID:29670018
Duplication and diversification of lectin receptor-like kinases (LecRLK) genes in soybean. PMID:29651041
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Two Phytoplasmas Elicit Different Responses in the Insect Vector Euscelidius variegatus Kirschbaum. PMID:29531134
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PMID:29474435
Biofilm Formation by the Acidophile Bacterium Acidithiobacillus thiooxidans Involves c-di-GMP Pathway and Pel exopolysaccharide. PMID:29466318
Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. PMID:29414762
Activation of Aflatoxin Biosynthesis Alleviates Total ROS in Aspergillus parasiticus. PMID:29382166
Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.). PMID:29375602
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
A chelicerate-specific burst of nonclassical Dscam diversity. PMID:29351731
Specialized attachment structure of the fish pathogenic oomycete Saprolegnia parasitica. PMID:29342156
DmCatD, a cathepsin D-like peptidase of the hematophagous insect Dipetalogaster maxima (Hemiptera: Reduviidae): Purification, bioinformatic analyses and the significance of its interaction with lipophorin in the internalization by developing oocytes. PMID:29325877
Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. PMID:29324689
Molecular and Biochemical Characterization of Opisthorchis viverrini Calreticulin. PMID:29320819
Simultaneous Silencing of Xylanase Genes in Botrytis cinerea. PMID:29312413
Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study. PMID:29299133
Synectin promotes fibrogenesis by regulating PDGFR isoforms through distinct mechanisms. PMID:29263300
Improving the explainability of Random Forest classifier - user centered approach. PMID:29218882
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. PMID:29218866
Identification and Initial Characterization of the Effectors of an Anther Smut Fungus and Potential Host Target Proteins. PMID:29165363
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
Copy Number Variation and Expression Analysis Reveals a Nonorthologous Pinta Gene Family Member Involved in Butterfly Vision. PMID:29136137
Identification of a molecular pH sensor in coral. PMID:29093223
20 years of the SMART protein domain annotation resource. PMID:29040681
Conotoxins as Tools to Understand the Physiological Function of Voltage-Gated Calcium (CaV) Channels. PMID:29027927
Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability. PMID:29021403
Dissecting the molecular assembly of the Toxoplasma gondii MyoA motility complex. PMID:28972141
A Novel Calcium Uptake Transporter of Uncharacterized P-Type ATPase Family Supplies Calcium for Cell Surface Integrity in Mycobacterium smegmatis. PMID:28951477
Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. PMID:28923009
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. PMID:28882004
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era. PMID:28870165
Disclosing 3' UTR cis-elements and putative partners involved in gene expression regulation in Leishmania spp. PMID:28859096
Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii. PMID:28852583
Polymorphism and structure of style-specific arabinogalactan proteins as determinants of pollen tube growth in Nicotiana. PMID:28797243
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PMID:28787438
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. PMID:28756777
Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. PMID:28738779
Cloning and Characterization of ThSHRs and ThSCR Transcription Factors in Taxodium Hybrid 'Zhongshanshan 406'. PMID:28726763
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Structural and functional diversity of EF-hand proteins: Evolutionary perspectives. PMID:28707401
Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues. PMID:28642634
Evolutionary origin of type IV classical cadherins in arthropods. PMID:28623893
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1. PMID:28530709
On patterns and re-use in bioinformatics databases. PMID:28525546
Analysis of CFB, a cytokinin-responsive gene of Arabidopsis thaliana encoding a novel F-box protein regulating sterol biosynthesis. PMID:28505379
Novel β-Lactamase blaARL in Staphylococcus arlettae. PMID:28497118
ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. PMID:28472320
Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. PMID:28464870
Analysis of the potato calcium-dependent protein kinase family and characterization of StCDPK7, a member induced upon infection with Phytophthora infestans. PMID:28451820
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
Identification and analysis of mutational hotspots in oncogenes and tumour suppressors. PMID:28423505
GibbsCluster: unsupervised clustering and alignment of peptide sequences. PMID:28407089
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources. PMID:28272476
Ornithine Aminotransferase, an Important Glutamate-Metabolizing Enzyme at the Crossroads of Multiple Metabolic Pathways. PMID:28272331
Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium. PMID:28254969
A Review of Functional Motifs Utilized by Viruses. PMID:28248213
Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. PMID:28188228
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
Protein Bioinformatics Databases and Resources. PMID:28150231
Function annotation of peptides generated from the non-coding regions of D. melanogaster genome. PMID:28149056
A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin. PMID:28129393
The essential requirement of an animal heme peroxidase protein during the wing maturation process in Drosophila. PMID:28077066
Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes. PMID:28056773
The Papillomavirus Episteme: a major update to the papillomavirus sequence database. PMID:28053164
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. PMID:28004836
A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses. PMID:28000080
The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. PMID:27920201
Defining Substrate Specificities for Lipase and Phospholipase Candidates. PMID:27911408
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes. PMID:27852223
Molecular cloning, expression, IgE binding activities and in silico epitope prediction of Per a 9 allergens of the American cockroach. PMID:27840974
Phosphorylation of poly(rC) binding protein 1 (PCBP1) contributes to stabilization of mu opioid receptor (MOR) mRNA via interaction with AU-rich element RNA-binding protein 1 (AUF1) and poly A binding protein (PABP). PMID:27836661
Convert your favorite protein modeling program into a mutation predictor: "MODICT". PMID:27760515
Ohgata, the Single Drosophila Ortholog of Human Cereblon, Regulates Insulin Signaling-dependent Organismic Growth. PMID:27702999
Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation. PMID:27605130
Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold. PMID:27591855
Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. PMID:27590521
Genome-wide analysis of lectin receptor-like kinases in Populus. PMID:27580945
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. PMID:27565432
Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain. PMID:27556926
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PMID:27552220
RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP. PMID:27546789
A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PMID:27541139
Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host. PMID:27513322
Flavoprotein-Mediated Tellurite Reduction: Structural Basis and Applications to the Synthesis of Tellurium-Containing Nanostructures. PMID:27507969
N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries. PMID:27498768
Evolutionary and functional analysis of mulberry type III polyketide synthases. PMID:27487946
Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. PMID:27474723
Genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (Hordeum vulgare L.). PMID:27447459
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627
Loss of function of the Drosophila Ninein-related centrosomal protein Bsg25D causes mitotic defects and impairs embryonic development. PMID:27422905
LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. PMID:27387560
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Misannotation Awareness: A Tale of Two Gene-Groups. PMID:27379147
Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization. PMID:27342569
The Ensembl gene annotation system. PMID:27337980
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. PMID:27307636
Consensus protein design. PMID:27274091
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
Genome- wide characterization of Nuclear Factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach. PMID:27186017
The Immature Fiber Mutant Phenotype of Cotton (Gossypium hirsutum) Is Linked to a 22-bp Frame-Shift Deletion in a Mitochondria Targeted Pentatricopeptide Repeat Gene. PMID:27172184
High-performance web services for querying gene and variant annotation. PMID:27154141
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
TOPDOM: database of conservatively located domains and motifs in proteins. PMID:27153630
Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics. PMID:27123592
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. PMID:27087306
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. PMID:27039071
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. PMID:26994138
Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-d-riboflavin to the antibiotic roseoflavin. PMID:26913589
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). PMID:26911138
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PMID:26890609
Identification of new palmitoylated proteins in Toxoplasma gondii. PMID:26825284
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling. PMID:26772592
Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PMID:26751210
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo. PMID:26739052
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
Cloning and Characterization of Two Potent Kunitz Type Protease Inhibitors from Echinococcus granulosus. PMID:26645974
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution. PMID:26608058
Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in Vitro. PMID:26589801
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica. PMID:26531864
Protein O-Glucosyltransferase 1 (POGLUT1) Promotes Mouse Gastrulation through Modification of the Apical Polarity Protein CRUMBS2. PMID:26496195
A multi-objective optimization approach accurately resolves protein domain architectures. PMID:26458889
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PMID:26367006
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives. PMID:26284089
Amplitude spectrum distance: measuring the global shape divergence of protein fragments. PMID:26268224
OsPRR37 and Ghd7 are the major genes for general combining ability of DTH, PH and SPP in rice. PMID:26238949
Functional expression of a novel Kunitz type protease inhibitor from the human blood fluke Schistosoma mansoni. PMID:26238343
Molecular mechanisms of the non-coenzyme action of thiamin in brain: biochemical, structural and pathway analysis. PMID:26212886
Database of RNA binding protein expression and disease dynamics (READ DB). PMID:26210853
Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus. PMID:26180540
In-depth characterization of trypsin-like serine peptidases in the midgut of the sugar fed Culex quinquefasciatus. PMID:26174750
Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY. PMID:26157611
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene. PMID:26114108
Comparative Analysis of Apicoplast-Targeted Protein Extension Lengths in Apicomplexan Parasites. PMID:26114107
Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. PMID:26106978
IBS: an illustrator for the presentation and visualization of biological sequences. PMID:26069263
Looking below the surface of nicotinic acetylcholine receptors. PMID:26067101
The structure of hookworm platelet inhibitor (HPI), a CAP superfamily member from Ancylostoma caninum. PMID:26057788
Expression of active trypsin-like serine peptidases in the midgut of sugar-feeding female Anopheles aquasalis. PMID:26021986
Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content. PMID:25997498
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
Genome-wide identification and evolution of HECT genes in soybean. PMID:25894222
Amelotin: an enamel matrix protein that experienced distinct evolutionary histories in amphibians, sauropsids and mammals. PMID:25884299
Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. PMID:25853125
Can the natural diversity of quorum-sensing advance synthetic biology? PMID:25806368
Ankyrin domain of myosin 16 influences motor function and decreases protein phosphatase catalytic activity. PMID:25775934
FR database 1.0: a resource focused on fruit development and ripening. PMID:25725058
Identification of divergent WH2 motifs by HMM-HMM alignments. PMID:25616999
A Phospho-SIM in the Antiviral Protein PML is Required for Its Recruitment to HSV-1 Genomes. PMID:25513827
Identification of two missense mutations of ERCC6 in three Chinese sisters with Cockayne syndrome by whole exome sequencing. PMID:25463447
Molecular basis for DPY-30 association to COMPASS-like and NURF complexes. PMID:25456412
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
Bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of New World bipartite begomoviruses. PMID:25383632
WDSPdb: a database for WD40-repeat proteins. PMID:25348404
Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.). PMID:25344821
Homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism. PMID:25320445
Two structural motifs within canonical EF-hand calcium-binding domains identify five different classes of calcium buffers and sensors. PMID:25313560
Molecular cloning and in-silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765. PMID:25304397
SMART: recent updates, new developments and status in 2015. PMID:25300481
Chlorovirus Skp1-binding ankyrin repeat protein interplay and mimicry of cellular ubiquitin ligase machinery. PMID:25253343
tBRD-1 selectively controls gene activity in the Drosophila testis and interacts with two new members of the bromodomain and extra-terminal (BET) family. PMID:25251222
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. PMID:25220818
Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome. PMID:25214042
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. PMID:25185655
Developmentally-Dynamic Murine Brain Proteomes and Phosphoproteomes Revealed by Quantitative Proteomics. PMID:25177544
Expression of α-subunit of α-glucosidase II in adult mouse brain regions and selected organs. PMID:25131991
A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum. PMID:25118601
The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses. PMID:25063321
The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity. PMID:25049225
Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. PMID:25008052
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). PMID:25007843
Systems biology in the context of big data and networks. PMID:24982882
CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models. PMID:24978609
The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. PMID:24950179
C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses. PMID:24915771
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PMID:24901469
Apolipoprotein L2 contains a BH3-like domain but it does not behave as a BH3-only protein. PMID:24901046
In Silico Prediction of T and B Cell Epitopes of Der f 25 in Dermatophagoides farinae. PMID:24895543
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). PMID:24778629
Cloning and functional characterization of three branch point oxidosqualene cyclases from Withania somnifera (L.) dunal. PMID:24770414
Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses. PMID:24762235
Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity. PMID:24760183
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). PMID:24742296
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Extracellular DNA metabolism in Haloferax volcanii. PMID:24600440
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
Multimethylation of Rickettsia OmpB catalyzed by lysine methyltransferases. PMID:24497633
Functional understanding of the diverse exon-intron structures of human GPCR genes. PMID:24467758
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
InterProScan 5: genome-scale protein function classification. PMID:24451626
Transient fusion and selective secretion of vesicle proteins in Phytophthora nicotianae zoospores. PMID:24392285
A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. PMID:24337801
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
Graph representation of high-dimensional alpha-helical membrane protein data. PMID:24294896
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). PMID:24256031
The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. PMID:24209742
Differential expression of CPKs and cytosolic Ca2+ variation in resistant and susceptible apple cultivars (Malus x domestica) in response to the pathogen Erwinia amylovora and mechanical wounding. PMID:24192013
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
Two distinct sensing pathways allow recognition of Klebsiella pneumoniae by Dictyostelium amoebae. PMID:24128258
PPR proteins of green algae. PMID:24021981
Identification and characterization of a periplasmic aminoacyl-phosphatidylglycerol hydrolase responsible for Pseudomonas aeruginosa lipid homeostasis. PMID:23792962
A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization. PMID:23759984
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. PMID:23505298
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
The PROSITE database
PubMed citations: 303.
303 articles citing: The PROSITE database
Structure, function, and pathology of protein O-glucosyltransferases. PMID:33436558
Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson's disease. PMID:33402667
Structural characterization and in vitro lipid binding studies of non-specific lipid transfer protein 1 (nsLTP1) from fennel (Foeniculum vulgare) seeds. PMID:33277525
Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study. PMID:33256744
Contributions of protein microenvironment in tannase industrial applicability: An in-silico comparative study of pathogenic and non-pathogenic bacterial tannase. PMID:33241136
GPCR-PEnDB: a database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors. PMID:33216895
Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling. PMID:33080171
DeeplyEssential: a deep neural network for predicting essential genes in microbes. PMID:32998698
A new mode of NPR1 action via an NB-ARC-NPR1 fusion protein negatively regulates the defence response in wheat to stem rust pathogen. PMID:32544264
The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. PMID:32424221
Identifications, Characteristics, and Expression Patterns of Small Heat Shock Protein Genes in a Major Mulberry Pest, Glyphodes pyloalis (Lepidoptera: Pyralidae). PMID:32365175
The genome evolution and low-phosphorus adaptation in white lupin. PMID:32103018
In silico identification and assessment of insecticide target sites in the genome of the small hive beetle, Aethina tumida. PMID:32050907
A bacterial phyla dataset for protein function prediction. PMID:31921945
The peptide transporter 1a of the zebrafish Danio rerio, an emerging model in nutrigenomics and nutrition research: molecular characterization, functional properties, and expression analysis. PMID:31890051
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Molecular characterization and expression analysis reveal the roles of Cys2/His2 zinc-finger transcription factors during flower development of Brassica rapa subsp. chinensis. PMID:31776846
Molecular cloning of Gibel carp (Carassius auratus gibelio) complement component C3 and its expression profile after Cyprinid herpesvirus 2 infection. PMID:31723065
Transcriptional Structure of Petunia Clock in Leaves and Petals. PMID:31671570
The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent Emission. PMID:31426490
The Nuts and Bolts of PIN Auxin Efflux Carriers. PMID:31417597
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. PMID:31368486
Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells. PMID:31316139
Inhibition of N-myristoyltransferase1 affects dengue virus replication. PMID:30848105
Crystal structure of MICU2 and comparison with MICU1 reveal insights into the uniporter gating mechanism. PMID:30755530
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. PMID:30532075
SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PMID:30402352
Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. PMID:30239843
Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom (Scorpaena plumieri). PMID:30181739
SDADB: a functional annotation database of protein structural domains. PMID:29961821
Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. PMID:29663699
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. PMID:29339766
Analysis of viral diversity for vaccine target discovery. PMID:29322922
The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings. PMID:29305577
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis. PMID:28970579
Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine. PMID:28890846
C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility. PMID:28716093
How lipid droplets "TAG" along: Glycerolipid synthetic enzymes and lipid storage. PMID:28642195
The Ds1 Transposon Provides Messages That Yield Unique Profiles of Protein Isoforms and Acts Synergistically With Ds to Enrich Proteome Complexity via Exonization. PMID:28469376
A three-way approach for protein function classification. PMID:28234929
Identification and characterization of an efficient acyl-CoA: diacylglycerol acyltransferase 1 (DGAT1) gene from the microalga Chlorella ellipsoidea. PMID:28222675
Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera. PMID:27746792
Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia. PMID:27347683
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production. PMID:27143514
Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. PMID:27092185
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. PMID:27038623
Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi. PMID:26350613
Oncorhynchus mykiss pax7 sequence variations with comparative analyses against other teleost species. PMID:26090310
An Ebola virus-centered knowledge base. PMID:26055098
Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. PMID:25918715
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. PMID:25426780
CGI-58/ABHD5 is phosphorylated on Ser239 by protein kinase A: control of subcellular localization. PMID:25421061
Text mining in cancer gene and pathway prioritization. PMID:25392685
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target. PMID:25253464
RADB: a database of rheumatoid arthritis-related polymorphisms. PMID:25228593
Evolution of TNF-induced apoptosis reveals 550 My of functional conservation. PMID:24927546
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. PMID:24843788
A combined approach for genome wide protein function annotation/prediction. PMID:24564915
Quantitative characterization of protein tertiary motifs. PMID:24464316
An insight into the transcriptome of the digestive tract of the bloodsucking bug, Rhodnius prolixus. PMID:24416461
Sequence analysis, structure and binding site prediction of Sigma 1 receptor protein by in silico method. PMID:24391355
Spatial expression of transcription factors in Drosophila embryonic organ development. PMID:24359758
Molecular cloning and expression of CYP9A61: a chlorpyrifos-ethyl and lambda-cyhalothrin-inducible cytochrome P450 cDNA from Cydia pomonella. PMID:24351812
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PMID:24250794
Analysis of new functional profiles of protein isoforms yielded by ds exonization in rice. PMID:24137048
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis. PMID:23756993
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PMID:23754939
Discovery of catalases in members of the Chlamydiales order. PMID:23729651
The effect of gene overlapping on the rate of RNA virus evolution. PMID:23686658
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes. PMID:23326453
Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. PMID:23180766
The molecular clockwork of the fire ant Solenopsis invicta. PMID:23152747
Genome-wide comparison of FGFRL1 with structurally related surface receptors. PMID:23136609
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PMID:23082187
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. PMID:22925230
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. PMID:22911826
A novel mutation causing nephronophthisis in the Lewis polycystic kidney rat localises to a conserved RCC1 domain in Nek8. PMID:22899815
Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions. PMID:22737237
Structural analysis of SHARPIN, a subunit of a large multi-protein E3 ubiquitin ligase, reveals a novel dimerization function for the pleckstrin homology superfold. PMID:22549881
Genomic, proteomic and physiological characterization of a T5-like bacteriophage for control of Shiga toxin-producing Escherichia coli O157:H7. PMID:22514640
Abberent expression analysis of LMNA gene in hutchinson-gilford progeria syndrome. PMID:22493523
Characterization of a Trypanosoma brucei Alkb homolog capable of repairing alkylated DNA. PMID:22465611
Tri-domain bifunctional inhibitor of metallocarboxypeptidases A and serine proteases isolated from marine annelid Sabellastarte magnifica. PMID:22411994
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
An insight into the sialome of Simulium guianense (DIPTERA:SIMulIIDAE), the main vector of River Blindness Disease in Brazil. PMID:22182526
Genome characterization of the oleaginous fungus Mortierella alpina. PMID:22174787
The STARD9/Kif16a kinesin associates with mitotic microtubules and regulates spindle pole assembly. PMID:22153075
DISC1: Structure, Function, and Therapeutic Potential for Major Mental Illness. PMID:22116789
Pangolin expression influences the development of a morphological novelty: beetle horns. PMID:21998033
Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species. PMID:21860605
An insight into the sialotranscriptome and proteome of the coarse bontlegged tick, Hyalomma marginatum rufipes. PMID:21851864
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PMID:21799808
Prediction of N-myristoylation modification of proteins by SVM. PMID:21738315
Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors. PMID:21725005
NELL-1 binds to APR3 affecting human osteoblast proliferation and differentiation. PMID:21723284
The mouse B cell-specific mb-1 gene encodes an immunoreceptor tyrosine-based activation motif (ITAM) protein that may be evolutionarily conserved in diverse species by purifying selection. PMID:21688146
Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. PMID:21687411
Novel TMPRSS3 variants in Pakistani families with autosomal recessive non-syndromic hearing impairment. PMID:21534946
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
WildSpan: mining structured motifs from protein sequences. PMID:21453542
Decapentaplegic (dpp) regulates the growth of a morphological novelty, beetle horns. PMID:21399983
Energetics-based discovery of protein-ligand interactions on a proteomic scale. PMID:21338610
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. PMID:21287609
Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups. PMID:21255364
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
Prediction of a new class of RNA recognition motif. PMID:21082207
Insight into the salivary transcriptome and proteome of Dipetalogaster maxima. PMID:21058630
Identification of transmembrane protein 88 (TMEM88) as a dishevelled-binding protein. PMID:21044957
Genome-wide comparative gene family classification. PMID:20976221
Characterization of the functional domain of β2-microglobulin from the Asian seabass, Lates calcarifer. PMID:20949082
Evidence for the horizontal transfer of an unusual capsular polysaccharide biosynthesis locus in marine bacteria. PMID:20921143
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. PMID:20858292
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans. PMID:20799944
Calpain 3 is a rapid-action, unidirectional proteolytic switch central to muscle remodeling. PMID:20694146
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. PMID:20529918
RTX proteins: a highly diverse family secreted by a common mechanism. PMID:20528947
A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. PMID:20479005
The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. PMID:20463021
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
Insight into the Sialome of the Bed Bug, Cimex lectularius. PMID:20441151
Protein phosphatase 2B (PP2B, calcineurin) in Paramecium: partial characterization reveals that two members of the unusually large catalytic subunit family have distinct roles in calcium-dependent processes. PMID:20435698
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Semantic integration of data on transcriptional regulation. PMID:20427517
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. PMID:20420672
Knockdown of bicaudal C in zebrafish (Danio rerio) causes cystic kidneys: a nonmammalian model of polycystic kidney disease. PMID:20412683
The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. PMID:20226034
Siderophores are not involved in Fe(III) solubilization during anaerobic Fe(III) respiration by Shewanella oneidensis MR-1. PMID:20190086
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. PMID:20154676
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. PMID:20122268
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Identification of a c-di-GMP-regulated polysaccharide locus governing stress resistance and biofilm and rugose colony formation in Vibrio vulnificus. PMID:20065022
Mis-spliced transcripts of nicotinic acetylcholine receptor alpha6 are associated with field evolved spinosad resistance in Plutella xylostella (L.). PMID:20062520
Structural basis of chemokine sequestration by a tick chemokine binding protein: the crystal structure of the complex between Evasin-1 and CCL3. PMID:20041127
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach. PMID:19961575
Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. PMID:19943115
Evidence for a novel gene associated with human influenza A viruses. PMID:19917120
Thalidomide attenuates nitric oxide-driven angiogenesis by interacting with soluble guanylyl cyclase. PMID:19912234
Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases. PMID:19911309
Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin. PMID:19908157
The comprehensive microbial resource. PMID:19892825
PepX: a structural database of non-redundant protein-peptide complexes. PMID:19880386
A structure filter for the Eukaryotic Linear Motif Resource. PMID:19852836
Pathema: a clade-specific bioinformatics resource center for pathogen research. PMID:19843611
Novel putative glycosylphosphatidylinositol-anchored micronemal antigen of Plasmodium falciparum that binds to erythrocytes. PMID:19820120
Characterization of DUF724 gene family in Arabidopsis thaliana. PMID:19795213
Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid. PMID:19776150
The final step of hygromycin A biosynthesis, oxidation of C-5''-dihydrohygromycin A, is linked to a putative proton gradient-dependent efflux. PMID:19770276
Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis. PMID:19767422
A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. PMID:19761605
Structural and functional constraints in the evolution of protein families. PMID:19756040
The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family. PMID:19737383
Comparison of structure-based and threading-based approaches to protein functional annotation. PMID:19731377
Quaranfil, Johnston Atoll, and Lake Chad viruses are novel members of the family Orthomyxoviridae. PMID:19726499
Alternative splicing of the Anopheles gambiae nicotinic acetylcholine receptor, Agamalphabeta9, generates both alpha and beta subunits. PMID:19669815
Integrase-directed recovery of functional genes from genomic libraries. PMID:19596808
A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana. PMID:19590748
Eps8 regulates axonal filopodia in hippocampal neurons in response to brain-derived neurotrophic factor (BDNF). PMID:19564905
7TMRmine: a Web server for hierarchical mining of 7TMR proteins. PMID:19538753
Visualising biological data: a semantic approach to tool and database integration. PMID:19534744
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain. PMID:19505478
seeMotif: exploring and visualizing sequence motifs in 3D structures. PMID:19477961
Databases and QSAR for cancer research. PMID:19458762
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. PMID:19445703
Conservation and variability of West Nile virus proteins. PMID:19401763
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. PMID:19389731
Evolution based on domain combinations: the case of glutaredoxins. PMID:19321008
Structural conservation of a short, functional, peptide-sequence motif. PMID:19273121
GEF1 is a ciliary Sec7 GEF of Tetrahymena thermophila. PMID:19267341
Convergence pattern studies of folate receptor. PMID:19238241
A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PMID:19198654
Insight into the sialome of the Black Fly, Simulium vittatum. PMID:19166301
Novel localization of callose in the spores of Physcomitrella patens and phylogenomics of the callose synthase gene family. PMID:19155219
Why is the correlation between gene importance and gene evolutionary rate so weak? PMID:19132081
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
Structural analysis of linear and conformational epitopes of allergens. PMID:19121639
Novel nicotine oxidoreductase-encoding gene involved in nicotine degradation by Pseudomonas putida strain S16. PMID:19060159
MFS transportome of the human pathogenic yeast Candida albicans. PMID:19055746
The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis. PMID:19040736
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Of bars and rings: Hof1-dependent cytokinesis in multiseptated hyphae of Ashbya gossypii. PMID:19029253
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Characterisation of novel protein families secreted by muscle stage larvae of Trichinella spiralis. PMID:18992250
InterPro: the integrative protein signature database. PMID:18940856
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. PMID:18831785
Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PMID:18818722
Conserved and variant molecular and functional features of multiple egg yolk precursor proteins (vitellogenins) in white perch (Morone americana) and other teleosts. PMID:18766402
Differential screening identifies transcripts with depot-dependent expression in white adipose tissues. PMID:18721461
Regulation of catalase activity and gene expression during Phytophthora nicotianae development and infection of tobacco. PMID:18705863
Cell cycle kinases predicted from conserved biophysical properties. PMID:18704950
Conservation and variability of dengue virus proteins: implications for vaccine design. PMID:18698358
Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. PMID:18695247
An O-phosphotransferase catalyzes phosphorylation of hygromycin A in the antibiotic-producing organism Streptomyces hygroscopicus. PMID:18644964
Identification of putative functional motifs in viral proteins essential for human cytomegalovirus DNA replication. PMID:18618235
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Local function conservation in sequence and structure space. PMID:18604264
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. PMID:18590572
SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum. PMID:18578888
PURE: a webserver for the prediction of domains in unassigned regions in proteins. PMID:18554415
AMYPdb: a database dedicated to amyloid precursor proteins. PMID:18544157
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation. PMID:18524800
Structural answers and persistent questions about how nicotinic receptors work. PMID:18508600
Cyclic-di-GMP regulates extracellular polysaccharide production, biofilm formation, and rugose colony development by Vibrio vulnificus. PMID:18487410
The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. PMID:18477637
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. PMID:18460207
Discovering sequence motifs with arbitrary insertions and deletions. PMID:18437229
Comparative protein structure modeling using Modeller. PMID:18428767
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. PMID:18387204
The MoVIN server for the analysis of protein interaction networks. PMID:18387199
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634. PMID:18369189
Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia. PMID:18366740
A histidine-rich and cysteine-rich metal-binding domain at the C terminus of heat shock protein A from Helicobacter pylori: implication for nickel homeostasis and bismuth susceptibility. PMID:18364351
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. PMID:18331637
A novel GDP-dependent pyruvate kinase isozyme from Toxoplasma gondii localizes to both the apicoplast and the mitochondrion. PMID:18326043
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. PMID:18318901
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. PMID:18314547
Characterisation of 3' transgene insertion site and derived mRNAs in MON810 YieldGard maize. PMID:18306044
An integrated approach to inferring gene-disease associations in humans. PMID:18300252
Aligning sequences by minimum description length. PMID:18274649
Mycobacterial PE_PGRS proteins contain calcium-binding motifs with parallel beta-roll folds. PMID:18267304
Prediction of protein-protein interactions using protein signature profiling. PMID:18267299
Mouse and human La proteins differ in kinase substrate activity and activation mechanism for tRNA processing. PMID:18257391
Annotation and expression profiling of apoptosis-related genes in the yellow fever mosquito, Aedes aegypti. PMID:18252247
Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms. PMID:18245455
Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PMID:18231586
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Drosophila Pxt: a cyclooxygenase-like facilitator of follicle maturation. PMID:18216169
Gene characterization index: assessing the depth of gene annotation. PMID:18213364
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
NestedMICA as an ab initio protein motif discovery tool. PMID:18194537
A small protein from the bop-brp intergenic region of Halobacterium salinarum contains a zinc finger motif and regulates bop and crtB1 transcription. PMID:18179416
Discovery of a novel class of highly conserved vaccine antigens using genomic scale antigenic fingerprinting of pneumococcus with human antibodies. PMID:18166586
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. PMID:18165317
Evaluating deterministic motif significance measures in protein databases. PMID:18157916
Regulation of rice NADPH oxidase by binding of Rac GTPase to its N-terminal extension. PMID:18156215
A molecular specificity code for the three mammalian KDEL receptors. PMID:18086916
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. PMID:18053145
A primer on python for life science researchers. PMID:18052533
Structure and function predictions of the Msa protein in Staphylococcus aureus. PMID:18047728
Robust recognition of zinc binding sites in proteins. PMID:18042678
Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PMID:17971876
Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus. PMID:17944850
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. PMID:17941992
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
The cys-loop ligand-gated ion channel gene superfamily of the red flour beetle, Tribolium castaneum. PMID:17880682
Evolutionary conservation of P-selectin glycoprotein ligand-1 primary structure and function. PMID:17868453
A homozygous mutation in a novel zinc-finger protein, ERIS, is responsible for Wolfram syndrome 2. PMID:17846994
The Ras-association domain family (RASSF) members and their role in human tumourigenesis. PMID:17692468
Predicting active site residue annotations in the Pfam database. PMID:17688688
Bacillus anthracis secretome time course under host-simulated conditions and identification of immunogenic proteins. PMID:17662140
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
HoxPred: automated classification of Hox proteins using combinations of generalised profiles. PMID:17626621
Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. PMID:17610133
Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity? PMID:17598909
Functional annotation strategy for protein structures. PMID:17597920
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. PMID:17594509
Clustering protein environments for function prediction: finding PROSITE motifs in 3D. PMID:17570144
The 2006 automated function prediction meeting. PMID:17570143
Differentiation-dependent expression of Adhfe1 in adipogenesis. PMID:17559793
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. PMID:17547750
MyHits: improvements to an interactive resource for analyzing protein sequences. PMID:17545200
Chemogenomic approaches to rational drug design. PMID:17533416
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. PMID:17430569
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis. PMID:17392363
HitKeeper, a generic software package for hit list management. PMID:17391514
Molecular basis for repression of liver X receptor-mediated gene transcription by receptor-interacting protein 140. PMID:17391100
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. PMID:17372208
Membrane protein prediction methods. PMID:17367718
The ring between ring fingers (RBR) protein family. PMID:17367545
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. PMID:17337525
Structure, interactions, and dynamics of the RING domain from human TRAF6. PMID:17327397
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Detection of conjugation related type four secretion machinery in Aeromonas culicicola. PMID:17205119
New developments in the InterPro database. PMID:17202162
Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock. PMID:17065608
Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. PMID:17064408
Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis. PMID:17054794
ORENZA: a web resource for studying ORphan ENZyme activities. PMID:17026747
DBC2 is essential for transporting vesicular stomatitis virus glycoprotein. PMID:17023000
The LRRK2 Gly2385Arg variant is associated with Parkinson's disease: genetic and functional evidence. PMID:17019612
Identification of a 709-amino-acid internal nonessential region within the essential conserved tegument protein (p)UL36 of pseudorabies virus. PMID:16973597
The cys-loop ligand-gated ion channel superfamily of the honeybee, Apis mellifera. PMID:16902773
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. PMID:16872539
ProSAT2--Protein Structure Annotation Server. PMID:16845114
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. PMID:16845026
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. PMID:16845025
MACSIMS: multiple alignment of complete sequences information management system. PMID:16792820
Predicting DNA-binding sites of proteins from amino acid sequence. PMID:16712732 -
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
PubMed citations: 6.
6 articles citing: pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. PMID:31631325
Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii. PMID:29114024
Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. PMID:25500536
HAMAP in 2015: updates to the protein family classification and annotation system. PMID:25348399
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157 - http://dx.doi.org/10.1093/nar/gks1067
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functional domain
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein identification
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2021-04-07T11:50:35.288810
gene and protein families
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
function analysis
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
sequence analysis
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2021-04-07T11:58:52.027751
Tags
More detailed information about this field from each metasource.
functional domain
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein domain
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein identification
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PROSITE; PROSITE; DOI: https://doi.org/10.25504/FAIRsharing.vwc6bd; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Apr 07 2021 11:38 a.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2021-04-07T11:50:35.288810
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2021-04-07T11:50:35.288810
gene and protein families
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
function analysis
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
sequence analysis
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
sequence sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2021-04-07T11:58:52.027751
functional domain molecular structure protein protein domain protein identification structure protein sequence protein sequence motifs and active sites gene and protein families function analysis sequence analysis sequence sites, features and motifs