Tag: protein sequence


Found 209 sources
Source Match ReputationScore*

UniProt Knowledgebase


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 ...
100%

Pfam


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 ...
77%

Conserved Domain Database


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 ...
62%

Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins


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 ...
59%

Simple Modular Architecture Research Tool


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 ...
59%

Integrated resource of protein families, domains and functional sites


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 ...
52%

PROSITE


PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
52%

Transporter Classification Database


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 ...
50%

PhosphoSite Plus


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.
49%

MetaCyc


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 ...
49%

Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups


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 ...
48%

ConoServer


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 ...
48%

InParanoid


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 ...
46%

Information system for G protein-coupled receptors (GPCRs)


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. ...
45%

LIPID MAPS


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 ...
45%

ProDom


ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
44%

Restriction enzymes and methylases 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 ...
44%

The Protein Database


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.
43%

Orthologous MAtrix


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 ...
43%

BindingDB database of measured binding affinities


BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH.
42%

PRINTS


PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family.
41%

MatrixDB: Extracellular Matrix Interaction Database


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 ...
41%

Database of Orthologous Groups


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 ...
41%

MobiDB


A database of protein disorder and mobility annotations. MobiDB was designed to offer a centralized resource for annotations of intrinsic protein disorder. The database features three levels of annotation: manually curated, indirect and predicted. Ma ...
41%

TIGRFAMs


TIGRFAMs collates multiple sequence alignments, protein sequence classification using Hidden Markov Models as well as the information that will assist the automated annotation of (mostly prokaryotic) proteins. TIGRFAMs was last updated in 2014.
40%

Termini-Oriented Protein Function INferred Database


TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alte ...
39%

OrtholugeDB


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 ...
39%

ARAMEMNON


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 ...
37%

ProtoNet


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.
37%

BAliBASE


BAliBASE; a benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.
37%

Bacterial protein tYrosine Kinase database


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.
37%

Major Intrinsic Proteins Modification Database


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.
36%

The human DEPhOsphorylation Database


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 ...
36%

Bactibase: database dedicated to bacteriocins


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 ...
36%

RBPDB


RNA-binding proteins and their specificities
36%

short Open Reading Frame database


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 ...
35%

PHOSIDA


Phosphorylation sites in various species identified by mass spectrometry
35%

Mammalian Protein Localization Database


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.
35%

PIR SuperFamily


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.
35%

Mimotope Database


Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucle ...
35%

MoonProt


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 ...
35%

Human Histone Database


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.
35%

Non-Ribosomal Peptides Database


Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.
35%

MiCroKiTS


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 ...
34%

PSORTdb


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 ...
33%

dbPTM


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 ...
33%

PeroxiBase


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.
33%

Telomerase Database


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 ...
33%

NucleaRDB


Families of nuclear hormone receptors
33%

SuperCYP


Cytochrome P450 alleles and drug interactions
33%

PeroxisomeDB


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.
33%

CLIPZ


Experimentally-determined binding sites of RNA-binding proteins
33%

cpnDB


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 ...
32%

KnotProt: A database of proteins with knots and slipknots


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 ...
32%

Knottin database


The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the "Inhibitor Cystine Knot (ICK) motif/family/fold").
32%

VDJdb: a curated database of T-cell receptors with known antigen specificity


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 ...
32%

SitEx database of eukaryotic protein functional sites


SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in ...
32%

Polbase


Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases.
32%

CentrosomeDB


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 ...
32%

PRIDB


Protein-RNA Interface Database
31%

PREX


PeroxiRedoxin classification indEX
31%

FireDB


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.
31%

Olfactory Receptor Database


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.
31%

HHMD


Human Histone Modification Database
31%

COMBREX


Computational Bridge to Experiments
31%

Death Domain Database


Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.
30%

Prokaryotic Glycoproteins Database


ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized eubacterial and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort ...
30%

gpDB


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 ...
30%

PLANT-PIs


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 ...
30%

OMPdb


Beta-barrel outer membrane proteins from Gram-negative bacteria
30%

ThYme


Thioester-active enzymes
30%

RNA Binding Protein Variant Database


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.
29%

CharProtDB


Experimentally Characterized Protein annotations
29%

LocDB


Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
29%

ProRepeat: An Integrated Repository for Studying Amino Acid Tandem Repeats in Proteins


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 ...
29%

FunShift


Functional divergence between the subfamilies of a protein domain family
29%

ADPriboDB


ADP-ribosylated proteins and sites
29%

PolyQ


Polyglutamine Repeats in Proteins
29%

MeMotif


Linear motifs in alpha-helical transmembrane proteins
29%

TMPad


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 ...
29%

SIMAP


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 ...
28%

TRIP


Protein-protein interactions for mammalian TRP channels
28%

REFOLD


The REFOLD database: a tool for the optimization of protein expression and refolding.
28%

VKCDB - Voltage-gated K+ Channel Database


Voltage-gated potassium channel database
28%

mutLBSgeneDB


Mutations in Ligand Binding Sites gene DataBase
28%

Transmembrane Helices in Genome Sequences


A web based database of Transmembrane Helices in Genome Sequences.
27%

Functional Coverage of the Proteome


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 ...
27%

Laminin Database


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 ...
27%

3DIV


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 ...
26%

UniParc


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 ...
26%

UniRef


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 ...
26%

PIR - Protein Information Resource


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 ...
24%

PANDIT


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 ...
24%

Cyanolyase


Sequences and motifs of the phycobilin lyase protein family
24%

Protein Classification Benchmark Collection


The Protein Classification Benchmark Collection was created in order to create standard datasets on which the performance of machine learning methods can be compared.
24%

Lipase Engineering 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 ...
24%

SISYPHUS


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 ...
24%

Phospho3D


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 ...
24%

KLIFs


Kinase-ligand Interaction Fingerprints and Structures
24%

TopDB


Topology Data Bank of transmembrane proteins
24%

SwissSidechain


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.
24%

UCSD-Nature Signaling Gateway Molecule Pages


Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling
24%

HIV RT and Protease Sequence Database


The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogues evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, ...
24%

UniSave


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 ...
24%

SuperSite


Dictionary of binding sites in proteins
23%

ProTeus


Signature sequences at the protein N- and C-termini
23%

Protein Clusters


Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes
23%

CoPS


Comprehensive peptide signature database
23%

InterDom


Putative protein domain interactions
23%

PDBSite


3D structure of protein functional sites
23%

Uniclust


Clustered protein sequences and multiple sequence alignments
23%

LenVarDB


Database of length variantion in protein domains
23%

Protein kinase resource


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 ...
23%

iPfam


A database of Pfam domain interactions
23%

MegaMotifbase


Structural motifs in protein families and superfamilies
23%

Minimotif Miner


Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules
23%

TOPPR


The Online Protein Processing Resource
23%

Secreted Protein Database


Secreted proteins from human, mouse and rat
23%

Heme Protein Database


Heme types, protein structures, axial ligands and Em values
23%

eProS


Energy profiles of protein structures
23%

ValidNESs


23%

O-GLYCBASE


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 ...
23%

PPT-DB


Protein Property Prediction and Testing Database
23%

PRF


Protein research foundation database of peptides: sequences, literature and unnatural amino acids
23%

RPG - Ribosomal Protein Gene database


Ribosomal protein gene database
23%

Kinomer


Classification of protein kinases encoded in various eukatotic species
23%

MALISAM


Manual alignments for structurally analogous motifs in proteins
23%

OPTIC


Orthologous and Paralogous Transcripts in Clades
23%

Membranome


A database of single-pass membrane proteins
23%

DoBISCUIT


Database Of BIoSynthesis clusters CUrated and InTegrated
23%

eF-site - Electrostatic surface of Functional site


Electrostatic potentials and hydrophobic properties of the active sites
23%

WDSPdb


WD40 domain structure predictions
23%

SelenoDB


A database of selenoprotein genes, proteins and SECIS elements
23%

DAnCER


Disease-Annotated Chromatin Epigenetics Resource
23%

ChromDB


Chromatin-associated proteins in a broad range of organisms
23%

Hits


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 ...
23%

NPD - Nuclear Protein Database


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 ...
23%

PlantTribes


Families of protein-coding genes from five sequenced plant species
23%

PLPMDB


Pyridoxal-5'-phosphate dependent enzymes mutations
23%

UUCD


Ubiquitin and ubiquitin-like conjugation database
23%

Ribonuclease P Database


RNase P sequences, alignments, and structures
23%

iProLINK


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 ...
23%

PHYTOPROT


Clusters of predicted plant proteins
23%

KIDFamMap


Kinase-inhibitor-disease family map
23%

NRichD


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 ...
23%

PyIgClassify


Clusters of conformations of antibody CDRs
23%

PA-GOSUB


Protein sequences from model organisms, GO assignment and subcellular localization
23%

ZiFDB


Zinc Finger DataBase
23%

WERAM


Writers, Erasers and Readers of Histone Acetylation and Methylation
23%

RaftProt


Lipid raft associated proteins in mammals
23%

TransportDB


Sequences and classification of predicted membrane transporters encoded in complete genomes
23%

Animal Toxin Database


Database of animal toxins
23%

ADDA - A Domain Database


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 ...
23%

iProClass


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 ...
23%

Degradome Database


Proteases, protease inhibitors and protease mutations in human, chimpanzee, mouse, and rat
23%

PIDD


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 ...
23%

EENdb


Engineered endonucleases: zinc finger nucleases and transcription activator-like effector nucleases
23%

PINT


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 ...
23%

PALI


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 ...
23%

MP:PD


Membrane Proteins: Packing Densities, packing defects and internal water molecules
23%

PhyloFacts


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 ...
23%

NBDB


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 ...
23%

MulPSSM


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 ...
23%

SEVENS


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 ...
23%

COMe - Co-Ordination of Metals etc.


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 ...
23%

OKCAM - now available at RhesusBase


Ontology-based Knowledgebase for Cell Adhesion Molecules
23%

Peptaibol


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 ...
23%

ASC - Active Sequence Collection


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 ...
23%

ProRule


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 ...
23%

Cybase


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 ...
23%

eSLDB - eukaryotic Subcellular Localization database


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 ...
23%

PRTAD


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 ...
23%

3DSwap: Database of Proteins involved in 3D domain Swapping


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 ...
23%

ProTherm


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 ...
23%

NMPdb - Nuclear matrix associated proteins database


Nuclear matrix associated proteins database
23%

CyMoBase


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 ...
23%

eBLOCKS


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 ...
23%

PPD


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 ...
23%

PFD - Protein Folding Database


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 ...
23%

SUPFAM


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 ...
23%

DescribePROT


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 ...
23%

NURSA


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 ...
23%

HRaP - Database of occurrence of HomoRepeats and Patterns in proteomes


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 ...
23%

SENTRA


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 ...
23%

Defensins Knowledgebase


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 ...
23%

DomIns - Database of Domain Insertions


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. ...
23%

BIOZON


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 ...
23%

SBASE


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 ...
23%

LOX-DB


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) ...
23%

CREMOFAC


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 ...
23%

NOPdb: Nucleolar Proteome Database


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 ...
23%

SUBA


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 ...
23%

SDAP


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 ...
23%

Wnt Database


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 ...
23%

EukProt


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 ...
23%

EVEREST - EVolutionary Ensembles of REcurrent SegmenTs


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 ...
23%

GPCR NaVa database


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 ...
23%

RNRdb


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 ...
23%

NESbase


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 ...
23%

iUUCD


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 ...
23%

SRPDB


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 ...
23%

PlantsP/PlantsT


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 ...
23%

DSD


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 ...
23%

CSDBase - Cold Shock Domain database


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 ...
23%

NLSdb


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 ...
23%

EROP-Moscow


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 ...
23%

AAindex


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 ...
23%

OGRe - Organellar Genome Retrieval


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 ...
23%

InterFil


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 ...
23%

*ReputationScore indicates how established a given datasource is. Find out more.




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