ProtoNet
Names
More detailed information about this field from each metasource.
ProtoNet
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
protonet
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
Names
More detailed information about this field from each metasource.
ProtoNet
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
protonet
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:17.258211
Names
More detailed information about this field from each metasource.
ProtoNet
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
protonet
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:17.258211
This source may no longer be available. No known URL could be resolved successfully.
This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.
Description
More detailed information about this field from each metasource.
This resource is a hierarchical clustering of UniProt protein sequences into hierarchical trees. This resource allows for the study of sub-family and super-family of a protein, using UniRef50 clusters.
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Hierarchical clustering of SWISS-PROT proteins
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Automatic hierarchical classification of protein sequences.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:17.258211
Webpage:
http://www.protonet.cs.huji.ac.il/Webpage
More detailed information about this field from each metasource.
http://www.protonet.cs.huji.ac.il/
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
Publications:
(12)
Publications
More detailed information about this field from each metasource.
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
PMID: 18586742
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet: hierarchical classification of the protein space
PMID: 12520020
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet 4.0: a hierarchical classification of one million protein sequences
PMID: 15608180
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
PMID: 22121228
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
A functional hierarchical organization of the protein sequence space
PMID: 15596019
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Functional annotation prediction: all for one and one for all
PMID: 16672244
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet: charting the expanding universe of protein sequences
PMID: 23563419
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
A robust method to detect structural and functional remote homologues
PMID: 15382232
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Connect the dots: exposing hidden protein family connections from the entire sequence tree
PMID: 18689824
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Fishing with (Proto)Net-a principled approach to protein target selection
PMID: 18629007
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR1027
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkr1027
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
Publications
More detailed information about this field from each metasource.
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
PMID: 18586742
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet: hierarchical classification of the protein space
PMID: 12520020
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet 4.0: a hierarchical classification of one million protein sequences
PMID: 15608180
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
PMID: 22121228
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
A functional hierarchical organization of the protein sequence space
PMID: 15596019
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Functional annotation prediction: all for one and one for all
PMID: 16672244
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
ProtoNet: charting the expanding universe of protein sequences
PMID: 23563419
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
A robust method to detect structural and functional remote homologues
PMID: 15382232
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Connect the dots: exposing hidden protein family connections from the entire sequence tree
PMID: 18689824
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Fishing with (Proto)Net-a principled approach to protein target selection
PMID: 18629007
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/GKR1027
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkr1027
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:17.258211
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Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
PubMed citations: 41.
41 articles citing: Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
Clustering biological sequences with dynamic sequence similarity threshold. PMID:35354426
Radiomics: A Primer on Processing Workflow and Analysis. PMID:35339254
Assessment of population structure, genetic diversity and relationship of Mediterranean olive accessions using SSR markers and computational tools. PMID:34761348
Linking genotype to phenotype in multi-omics data of small sample. PMID:34256701
A Deep Learning Approach to Antibiotic Discovery. PMID:32084340
Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans. PMID:31959995
Molecular Cavity Topological Representation for Pattern Analysis: A NLP Analogy-Based Word2Vec Method. PMID:31795343
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils. PMID:30808694
Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey. PMID:29520122
Hemimetabolous genomes reveal molecular basis of termite eusociality. PMID:29403074
HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. PMID:29315405
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Annotation of nerve cord transcriptome in earthworm Eisenia fetida. PMID:29204349
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. PMID:27803195
Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment. PMID:27761315
Clustering analysis of proteins from microbial genomes at multiple levels of resolution. PMID:27586436
High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons. PMID:26593439
Clustering Acoustic Segments Using Multi-Stage Agglomerative Hierarchical Clustering. PMID:26517376
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. PMID:26475107
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Ribosomal Database Project: data and tools for high throughput rRNA analysis. PMID:24288368
FunGene: the functional gene pipeline and repository. PMID:24101916
Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. PMID:23805789
Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. PMID:23639576
ProtoNet: charting the expanding universe of protein sequences. PMID:23563419
DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PMID:23554899
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PMID:23093919
A novel hierarchical clustering algorithm for gene sequences. PMID:22823405
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. PMID:21622657
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. PMID:21612636
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
Genome-wide comparative gene family classification. PMID:20976221
Sequence embedding for fast construction of guide trees for multiple sequence alignment. PMID:20470396
SPICi: a fast clustering algorithm for large biological networks. PMID:20185405
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231 -
ProtoNet: hierarchical classification of the protein space
PubMed citations: 35.
35 articles citing: ProtoNet: hierarchical classification of the protein space
Integrated bioinformatics based subtractive genomics approach to decipher the therapeutic function of hypothetical proteins from Salmonella typhi XDR H-58 strain. PMID:35037232
Gene regulation in Kluyveromyces marxianus in the context of chromosomes. PMID:29346402
Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets. PMID:29212526
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. PMID:26774999
Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications. PMID:26462798
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens. PMID:25437336
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
A pluralistic account of homology: adapting the models to the data. PMID:24273322
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
Proteomic properties reveal phyloecological clusters of Archaea. PMID:23133575
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. PMID:22070249
Family classification without domain chaining. PMID:19478015
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
Global considerations in hierarchical clustering reveal meaningful patterns in data. PMID:18493326
Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis. PMID:17906152
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space? PMID:17112376
The Escherichia coli proteome: past, present, and future prospects. PMID:16760308
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Functional annotation prediction: all for one and one for all. PMID:16672244
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. PMID:16436801
SIMAP: the similarity matrix of proteins. PMID:16381858
ProTeus: identifying signatures in protein termini. PMID:15980469
Large scale hierarchical clustering of protein sequences. PMID:15663796
ProtoNet 4.0: a hierarchical classification of one million protein sequences. PMID:15608180
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. PMID:15608172
Progress towards mapping the universe of protein folds. PMID:15128436
PHYTOPROT: a database of clusters of plant proteins. PMID:14681432
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. PMID:14500825 -
ProtoNet 4.0: a hierarchical classification of one million protein sequences
PubMed citations: 29.
29 articles citing: ProtoNet 4.0: a hierarchical classification of one million protein sequences
Clustering analysis of proteins from microbial genomes at multiple levels of resolution. PMID:27586436
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles. PMID:24246499
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. PMID:24065691
How to inherit statistically validated annotation within BAR+ protein clusters. PMID:23514411
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
DAMPD: a manually curated antimicrobial peptide database. PMID:22110032
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. PMID:21622657
Genome-wide comparative gene family classification. PMID:20976221
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes. PMID:20823311
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. PMID:20444873
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
ESG: extended similarity group method for automated protein function prediction. PMID:19435743
ClanTox: a classifier of short animal toxins. PMID:19429697
Partitioning clustering algorithms for protein sequence data sets. PMID:19341454
Protein function annotation by homology-based inference. PMID:19226439
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
SIMAP--structuring the network of protein similarities. PMID:18037617
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. PMID:16481312
JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture. PMID:16135248
ProTarget: automatic prediction of protein structure novelty. PMID:15980586
ProTeus: identifying signatures in protein termini. PMID:15980469
A functional hierarchical organization of the protein sequence space. PMID:15596019 -
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
PubMed citations: 22.
22 articles citing: ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94. PMID:32834707
Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens' Minisatellite 33.15-Tagged Transcript pAKT-45 Variants. PMID:32566673
Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis. PMID:30602087
A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. PMID:29785196
Small Myristoylated Protein-3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis. PMID:29301342
Percolation in protein sequence space. PMID:29261740
Overlooked Short Toxin-Like Proteins: A Shortcut to Drug Design. PMID:29109389
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. PMID:28324524
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. PMID:28324295
Protein Bioinformatics Databases and Resources. PMID:28150231
Evaluation of a hypothetical protein for serodiagnosis and as a potential marker for post-treatment serological evaluation of tegumentary leishmaniasis patients. PMID:28150041
Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors. PMID:27729842
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension. PMID:25813999
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Integrating in silico resources to map a signaling network. PMID:24233784
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. PMID:24165881
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
ProtoNet: charting the expanding universe of protein sequences. PMID:23563419
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
The use of evolutionary patterns in protein annotation. PMID:22633559 -
A functional hierarchical organization of the protein sequence space
PubMed citations: 14.
14 articles citing: A functional hierarchical organization of the protein sequence space
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
High-throughput genome scaffolding from in vivo DNA interaction frequency. PMID:24270850
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
Gene cluster statistics with gene families. PMID:19150803
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
Global considerations in hierarchical clustering reveal meaningful patterns in data. PMID:18493326
Discovering multi-level structures in bio-molecular data through the Bernstein inequality. PMID:18387206
Model order selection for bio-molecular data clustering. PMID:17493256
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Functional annotation prediction: all for one and one for all. PMID:16672244
The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03. PMID:16511166
ProTarget: automatic prediction of protein structure novelty. PMID:15980586
ProTeus: identifying signatures in protein termini. PMID:15980469 -
Functional annotation prediction: all for one and one for all
PubMed citations: 12.
12 articles citing: Functional annotation prediction: all for one and one for all
Protein function prediction with gene ontology: from traditional to deep learning models. PMID:34513334
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Seq2Ref: a web server to facilitate functional interpretation. PMID:23356573
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
GOPred: GO molecular function prediction by combined classifiers. PMID:20824206
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. PMID:20444873
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PMID:19247487
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
Functional annotation strategy for protein structures. PMID:17597920
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
New avenues in protein function prediction. PMID:16731984 -
ProtoNet: charting the expanding universe of protein sequences
PubMed citations: 7.
7 articles citing: ProtoNet: charting the expanding universe of protein sequences
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
Hemimetabolous genomes reveal molecular basis of termite eusociality. PMID:29403074
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. PMID:26774999
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
NeuroPID: a classifier of neuropeptide precursors. PMID:24792159 -
A robust method to detect structural and functional remote homologues
PubMed citations: 5.
5 articles citing: A robust method to detect structural and functional remote homologues
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Functional annotation prediction: all for one and one for all. PMID:16672244
ProtoNet 4.0: a hierarchical classification of one million protein sequences. PMID:15608180
A functional hierarchical organization of the protein sequence space. PMID:15596019 -
Connect the dots: exposing hidden protein family connections from the entire sequence tree
PubMed citations: 4.
4 articles citing: Connect the dots: exposing hidden protein family connections from the entire sequence tree
Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. PMID:23805789
Prediction of mucin-type O-glycosylation sites by a two-staged strategy. PMID:20652405
ESG: extended similarity group method for automated protein function prediction. PMID:19435743
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790 -
Fishing with (Proto)Net-a principled approach to protein target selection
PubMed citations: 0.
0 articles citing: Fishing with (Proto)Net-a principled approach to protein target selection
- http://dx.doi.org/10.1093/nar/GKR1027
- http://dx.doi.org/10.1093/nar/gkr1027
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More detailed information about this field from each metasource.
cross linking
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
peptide property
metasource: Fairsharing.org
version: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:17.258211
Tags
More detailed information about this field from each metasource.
cross linking
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
enzyme
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
peptide property
metasource: Fairsharing.orgversion: FAIRsharing.org: ProtoNet; ProtoNet; DOI: https://doi.org/10.25504/FAIRsharing.wv5q9d; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:17.258211
cross linking enzyme gene ontology enrichment peptide property protein sequence protein domains and classification gene and protein families
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