Tag: protein sequence

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...

InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as si ...

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of geneti ...

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function ...

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.

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the gene ...

This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for clas ...

PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are fi ...

The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIP ...

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. ...

The InParanoid database provides a user interface to orthologs inferred by the InParanoid algorithm. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteom ...

The Stanford HIV Drug Resistance Database (HIVDB) is an essential resource for public health officials monitoring ADR and TDR, for scientists developing new ARV drugs, and for HIV care providers managing patients with HIVDR.

The UniProt Reference Clusters are three separate datasets that compress sequence space at different resolutions, achieved by merging sequences and sub-sequences that are 100% (UniRef100), >=90% (UniRef90), or >=50% (UniRef50) identical, regardless o ...

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.

The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability ...

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database ...

TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene s ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family. A fingerprint is a group of conserved motifs used to characterize a protein family. Usually, the motifs do not overlap, though they ma ...

The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...

OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ort ...

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

MoonProt Database is a manually curated, searchable, internet-based resource with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. Moonlighting proteins comprise a class of multifunctional pr ...

The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.

ARAMEMNON is a curated database for Arabidopsis thaliana transmembrane (TM) proteins and transporters. The database compiles topology and signal sequence predictions and displays the results in a directly comparable graphical output format for presen ...

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

BAliBASE; a benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.

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.

BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships str ...

RNA-binding proteins and their specificities

This is a database of comparative protein structure models of the MIP (Major Intrinsic Protein) family of proteins. The MIPs have been identified from the completed genome sequence of organisms available at NCBI.

sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are pro ...

Phosphorylation sites in various species identified by mass spectrometry

HIstome (Human histone database) is a freely available, specialist, electronic database dedicated to display information about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes.

The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.

The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity in ...

This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musc ...

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences.

Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and aids identification of potential cell surface diagnostic markers, drug targets, or vaccine components. PSORTdb comprises ePSORTdb, a manual ...

Families of nuclear hormone receptors

Cytochrome P450 alleles and drug interactions

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

Experimentally-determined binding sites of RNA-binding proteins

Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, and in bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some ...

KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The da ...

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

CentrosomeDB is a collection of human and drosophila centrosomal genes that were reported in the literature and other sources. The database offers the possibility to study the evolution, function, and structure of the centrosome. They have compiled i ...

The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the "Inhibitor Cystine Knot (ICK) motif/family/fold").

Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases.

Protein-RNA Interface Database

PeroxiRedoxin classification indEX

Mimotope database, active site-mimicking peptides selected from phage-display libraries

ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family.

fireDB is a database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords.

Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.

Human Histone Modification Database

Computational Bridge to Experiments

Plant protease inhibitors (PIs) can be counted among the defensive proteins that plants display to minimize the adverse effects deriving from the attack of phytophagous insects. They are usually present in seeds and storage tissues, but are also expr ...

REFOLDdb is a resource for the optimization of protein refolding, referring to published methods employed in the refolding of recombinant proteins. It stores a collection of published experimental approaches and records for refolding proteins. It con ...

Beta-barrel outer membrane proteins from Gram-negative bacteria

GpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive liter ...

RBP-Var is a database of functional variants involved in regulation mediated by RNA-binding proteins. Human genome variants can change the RNA structure and affect RNA-protein interactions.

Thioester-active enzymes

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together wit ...

Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

Experimentally Characterized Protein annotations

Functional divergence between the subfamilies of a protein domain family

Polyglutamine Repeats in Proteins

Protein-protein interactions for mammalian TRP channels

The TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins. TMPad includes geometric descriptors of helix ...

Protein sequences are of utmost importance for studying the function and evolution of genes and genomes. Therefore a rich collection of methods in computational biology relies on the analysis and comparison of protein sequences. Many of these intensi ...

Linear motifs in alpha-helical transmembrane proteins

Experimentally characterized Prokaryotic GlycoProteins

Voltage-gated potassium channel database

Mutations in Ligand Binding Sites gene DataBase

The Lipase Engineering Database (http://www.led.uni-stuttgart.de) integrates information on sequence, structure, and function of lipases, esterases, and related proteins. Sequence data on 806 protein entries are assigned to 38 homologous families, wh ...

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play ...

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

DescribePROT is a database containing annotations of 13 putative structural and functional properties at the amino acid level for ~1.4 million proteins from 83 popular/model organism, to be extended to hundreds of additional organisms. Users can sear ...

A web based database of Transmembrane Helices in Genome Sequences.

FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes and nuclear receptors, offering both graphical and quantitative data on th ...

Projections of protein functional Sites on Exons

Laminins (LM) correspond to a large number of heretotrimeric glycoproteins, playing and a major role in several cell functions, including differentiation, proliferation, adhesion, and migration [1-3]. In addition to binding to other extracellular mat ...

dbPTM is a databases which accumulates the biological information related to protein post-translational modification (PTM), such as the catalytic sites, structural information, solvent accessibility of residues, protein secondary structures, protein ...

The UniProt archive (UniParc), part of the UniProt databases, is an archival protein sequence collection from all major publicly accessible resources. New and revised protein sequences are added daily into UniParc while not deleting the previous vers ...

The Protein Information Resource (PIR) is an integrated public bioinformatics resource that supports genomic and proteomic research and scientific studies. PIR has provided many protein databases and analysis tools to the scientific community, includ ...

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains the seed protein sequence alignments from the Pfam-A (curated families) database; nucleotide sequence alignments derived f ...

Sequences and motifs of the phycobilin lyase protein family

The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.

Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database als ...

The SISYPHUS database contains manually curated multiple structural alignments constructed for a set of proteins with known three-dimensional structures that have revealed non-trivial structural relationships and whose structural similarity is ambigu ...

Topology Data Bank of transmembrane proteins

SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.

Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling

The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot a nd UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries are loaded into the UniSave as part of the public UniProtK ...

Dictionary of binding sites in proteins

Signature sequences at the protein N- and C-termini

Comprehensive peptide signature database

Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes

Putative protein domain interactions

3D structure of protein functional sites

Clustered protein sequences and multiple sequence alignments

Database of length variantion in protein domains

The Protein Kinase Resource (PKR) is a curated information source which provides an integrated view of sequence and structure data combined with biochemical and genetic function data focused on a single family of proteins, the protein kinases. In add ...

A database of Pfam domain interactions

Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules

Structural motifs in protein families and superfamilies

The Online Protein Processing Resource

Secreted proteins from human, mouse and rat

Energy profiles of protein structures

Heme types, protein structures, axial ligands and Em values

O-GLYCBASE is a database of glycoproteins with O-linked and C-linked glycosylation sites. Entries with at least one experimentally verified glycosylation site have been compiled from protein sequence databases and literature. Each entry contains info ...

Protein Property Prediction and Testing Database

Protein research foundation database of peptides: sequences, literature and unnatural amino acids

Ribosomal protein gene database

Classification of protein kinases encoded in various eukatotic species

Manual alignments for structurally analogous motifs in proteins

Orthologous and Paralogous Transcripts in Clades

A database of single-pass membrane proteins

Electrostatic potentials and hydrophobic properties of the active sites

WD40 domain structure predictions

Database Of BIoSynthesis clusters CUrated and InTegrated

A database of selenoprotein genes, proteins and SECIS elements

Disease-Annotated Chromatin Epigenetics Resource

Chromatin-associated proteins in a broad range of organisms

The NPD is a curated database that contains information on more than 1200 vertebrate proteins that are thought, or are known, to localise to the cell nucleus. Each entry is annotated with information on predicted protein size and isoelectric point, a ...

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent ...

Families of protein-coding genes from five sequenced plant species

Ubiquitin and ubiquitin-like conjugation database

Pyridoxal-5'-phosphate dependent enzymes mutations

RNase P sequences, alignments, and structures

iProLINK (integrated Protein Literature, INformation and Knowledge) is a resource to facilitate text mining research in the area of literature-based database curation, named entity recognition, and protein ontology development. This collection of ann ...

Kinase-inhibitor-disease family map

Clusters of predicted plant proteins

Efficiency of protein remote homology detection methods depends on the dispersion of the protein sequence space and the availability of intermediate sequences between two related protein families. In the absence of any structural evidence and natural ...

Protein sequences from model organisms, GO assignment and subcellular localization

Clusters of conformations of antibody CDRs

Zinc Finger DataBase

Writers, Erasers and Readers of Histone Acetylation and Methylation

Lipid raft associated proteins in mammals

Sequences and classification of predicted membrane transporters encoded in complete genomes

Database of animal toxins

ADDA is a global clustering of protein sequences into protein domains and protein domain families. The database currently contains domains for 1.5 Mio sequences from UniProt, ENSEMBL, and other sequence databases. The domains are grouped into 123,000 ...

The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 175 biological databases, including databases for protein families, functions and pathways, interact ...

Proteases, protease inhibitors and protease mutations in human, chimpanzee, mouse, and rat

PIDD is a dedicated database and structural bio-informatics system for distance based protein modeling. The database is developed to host and analyze the statistical data for protein inter-atomic distances based on their distributions in databases of ...

Engineered endonucleases: zinc finger nucleases and transcription activator-like effector nucleases

The first release of Protein-protein Interactions Thermodynamic Database (PINT) contains more than 1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information. Each ...

Membrane Proteins: Packing Densities, packing defects and internal water molecules

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains structure-based sequence alignments and dendrograms based on information primarily derived from the structural alignments at domain level [1,2]. Protein domain d ...

The PhyloFacts resource contains pre-calculated structural and phylogenomic analysis of over 15,000 protein family "books" across the Tree of Life. Each book includes a multiple sequence alignment, one or more phylogenetic trees, predicted subfamilie ...

Seven-transmembrane-helix receptors (7-TMR), known as G-protein-coupled receptors [1], are important genes that work as the gateway of signal transudation induced by ligand binding. Recent progress in determination of human draft sequences [2,3] acce ...

NBDB database provides profiles of Elementary Functional Loops (EFLs) involved in binding of nucleotide-containing ligands. Each EFL in form of a PSSM (position-specific scoring matrix) profile is complemented with the information on SCOP entities, s ...

Representation of multiple sequence alignments of protein families in terms of Position Specific Scoring Matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the ...

COMe (Co-Ordination of Metals etc.) represents the classification of bioinorganic proteins. COMe consists of three types of entries: "bioinorganic motif", "molecule", and "complex protein"; each entry is assigned a unique identifier. A bioinorganic m ...

Ontology-based Knowledgebase for Cell Adhesion Molecules

The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. The database includes sequence, biological source, and bibliographical data for the naturally-occurring peptaibols. Information is also ...

ASC (Active Sequences Collection) is a database of short amino acid sequences with known biological activity. The current version is substantially improved as compared to the previous release; it now includes more than 1300 different active short pro ...

The ProRule database is a new section of PROSITE, which contains additional information about profiles. ProRule provides position specific-information about functionally and structurally relevant residues found in PROSITE profiles, as well as specifi ...

CyBase is a curated database and information source for backbone-cyclised proteins. The database incorporates naturally occurring cyclic proteins as well as synthetic derivatives, grafted analogues and acyclic permutants. The database provides a cent ...

eSLDB (eukaryotic Subcellular Localization DataBase) collects the annotations of subcellular localization of eukaryotic proteomes. For each sequence, the database lists localization obtained adopting three different approaches: 1) experimentally dete ...

ProThermDB is a database for proteins and mutants with data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant ...

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles, based on their distr ...

Protein oligomerization is a key biochemical step to perform the designated function of proteins. 3D domain swapping is a unique protein oligomerization phenomenon observed in a wide array of proteins involved in diverse functional roles. Apart from ...

Nuclear matrix associated proteins database

Classifying proteins into families and super-families allows identification of functionally mportant conserved domains. The motifs and scoring matrices derived from such conserved regions provide computational tools to recognize similar patterns in n ...

CyMoBase is an online database for manually annotated protein sequences of cytoskeletal and motor proteins and associated information. It currently offers more than 3000 sequences from 26 proteins in more than 350 species. Meta information linked to ...

The Protein Folding Database (PFD) is a searchable collection of all annotated structural, methodological, kinetic and thermodynamic data relating to experimental protein folding studies. The database structure allows visualization of folding data in ...

During the course of evolution, protein sequences derived from a common ancestor diverge by mutations, insertions and deletions, gene duplication and recombination and give rise to diverse families with no easily detectable sequence similarity. These ...

NURSA is a resource within which bioinformatic and bench research efforts in the field of nuclear receptors can be pursued in a synergistic and multidisciplinary approach, using a common technological platform. The primary directive of the NURSA prog ...

With active studying of disordered regions and their function we focus our attention on manifold long repeats of one amino acid (homorepeats) (1). Our database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kin ...

The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of over 350 defensin records each contain ...

Biozon is a platform that allows for the storage, management, and analysis of interrelated proteins, genes, interactions, protein families, cellular pathways and more. These heterogeneous data types and the relations between them are locally warehous ...

SENTRA (http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html) is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and meth ...

Proteins can be formed by single or multiple domains. The process of recombination at the molecular level has generated a wide variety of multi-domain proteins with specific domain organization to cater to the functional requirements of an organism. ...

SBASE (http://www.icgeb.trieste.it/sbase) is an on-line collection of protein domain sequences and related computational tools designed to facilitate detection of domain homologies based on simple database search. The tenth - "jubilee release" of the ...

CREMOFAC is a dedicated web-database for ATP and Non-ATP dependent chromatin-remodeling factors. The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. It provides in-depth inf ...

Due to their involvement in several diseases like cancer, inflammation, fever or arthritis, a lot of research is done on lipoxygenases yielding information about sequence, structure and function of these proteins. The LipOXygenases-DataBase (LOX-DB) ...

The Nucleolar Proteome Database (NOPdb) archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein e ...

The Arabidopsis Subcellular Database (SUBA, http://suba.plantenergy.uwa.edu.au) is maintained by the ARC Centre of Excellence in Plant Energy Biology at The University of Western Australia. The database contains publicly available protein subcellular ...

SDAP (Structural Database of Allergenic Proteins) is a Web server that provides rapid, cross-referenced assess to the sequences, structures, and IgE epitopes of allergenic proteins. The SDAP core is a series of CGI scripts that process the user queri ...

Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Wnt genes and Wnt signaling are also implicated in cancer. Insights into the mechanisms of Wnt action have emerg ...

EukProt is a database of published and publicly available predicted protein sets and unannotated genomes selected to represent eukaryotic diversity, including 742 species from all major supergroups as well as orphan taxa. The goal of the database is ...

EVEREST is an automatic computational process identifying protein domainsand classifying them into families. The EVEREST database contains 20,029families, each defined by one or more HMMER HMMs. EVEREST has beenthoroughly tested and evaluated, and ha ...

The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Vari ...

RNRdb - the Ribonucleotide Reductase Database - is a tool developed for ribonucleotide reductase (RNR) research. RNR is an enzyme that uses radical chemistry to reduce ribonucleotides to deoxyribonucleotides. Since this is the only pathway for the de ...

Protein export from the nucleus is often mediated by a Leucine-rich nuclear export signal (NES) consisting of 4-5 hydrophobic residues within a region of approximately 10 amino acids. Many Leucine-rich NESs have been identified and reported in litera ...

Signal recognition particle (SRP) is an ribonucleoprotein particle designed to recognize secretory signal sequences as they emerge from the ribosome. SRP associates with the SRP-receptor in the ER membrane, is released from the ribosome, and recycled ...

The ubiquitin and ubiquitin-like (Ub/Ubl) conjugation is one of the most important post- translational modifications (PTMs) in proteins, and regulates a large number of cellular processes, such as cell cycle, signal transduction, apoptosis and auto ...

As one database with two functionally different web interfaces, PlantsP and PlantsT are plant-specific curated databases that combine sequence derived information with experimental functional genomics data. PlantsP focuses on proteins involved in the ...

Dehydrogenase enzymes belong to the oxidoreductase class and utilise the coenzymes NAD and NADP. Stereo-selectivity is focused on the C4 hydrogen atoms of the nicotinamide ring of NAD(P). Depending upon which hydrogen is transferred at the C4 locatio ...

CSDBase (http://www.chemie.uni-marburg.de/~csdbase/) is an interactive Internet-embedded research platform providing detailed information on cold shock domain-containing proteins and bacterial cold shock responses. In its second release, access to CS ...

NLSdb is a database of nuclear localization signals (NLSs)and of nuclear proteins.NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus.The database contains 114 experimentally determined NLSs that were obtaine ...

Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from more than 1000 organisms representing all the biological kingdoms. We have compiled the known physi ...

AAindex is a database of amino acid indices and amino acid mutation matrices. An amino acid index is a set of 20 numerical values representing various physicochemical and biochemical properties of amino acids. An amino acid mutation matrix is general ...

OGRe is a relational database containing information on completely sequenced animal mitochondrial genomes. It currently contains 473 species. This is the full set of complete metazoan mitochondrial genomes available as of July 2004. The structure of ...

The Human Intermediate Filament Database (http://www.interfil.org) was initiated by the Human Genetics Unit, University of Dundee in 2001 and was revised by the Centre for Molecular Medicine and the Bioinformatics Institute in Singapore in 2006, from ...