PROTEIN DATABASES
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A Library of Protein Family Cores |
Structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures. |
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Assembly Converter |
Map (liftover) your data's coordinates to the current assembly |
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BioGPS biogps.org |
BioGPS is a gene portal built with two guiding principles in mind - customizability and extensibility. |
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CATH |
Protein Structure Classification database |
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CiteAb citeab.com |
CiteAb’s antibody and biochemical search engine provides a simple way for researchers to find reagents that work. |
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Data Slicer |
Get a subset of data from a BAM or VCF file |
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Database of Interacting Proteins |
Univ. of California |
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Interact |
An Object Oriented Database for Protein-Protein Interactions. |
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DisProt |
Database of experimental evidences of disorder in proteins (Indiana University School of Medicine, Temple University, University of Padua) |
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ExPASy Molecular Biology Server |
This is the ExPASy proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. |
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File Chameleon |
Convert Ensembl files for use with other analysis tools |
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guidetopharmacology.org |
This website is intended to become a “one-stop shop” portal to pharmacological information. The searchable database provides quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. It aims to offer accurate information on the basic science underlying drug action. |
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ID History Converter |
Convert a set of Ensembl IDs from a previous release into their current equivalents |
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InterPro |
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. |
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Linkage Disequilibrium Calculator |
Calculate LD between variants using genotypes from a selected population |
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locate.imb.uq.edu.au |
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. |
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mips.helmholtz-muenchen.de/corum |
Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM database is a collection of experimentally verified mammalian protein complexes. |
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MobiDB |
Database of intrinsic protein disorder annotation (University of Padua) |
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ModBase |
Database of comparative protein structure models (Sali Lab, UCSF) |
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NCBI |
Protein sequence and knowledgebase (National Center for Biotechnology Information) |
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neXtProt |
A human protein-centric knowledge resource |
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PaxDB pax-db.org |
PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues. |
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Pfam |
Protein families database of alignments and HMMs (Sanger Institute) |
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PIR – Protein Information Resource |
The Protein Information Resource (PIR), in collaboration with the Munich Information Center for Protein Sequences(MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database – a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available. |
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PIR-NREF |
The PIR-NREF is a Non-redundant REFerence protein database designed to provide a timely and comprehensive collection of all protein sequence data, keeping pace with the genome sequencing projects and containing source attribution and minimal redundancy. |
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PMD |
The Protein Mutant Database (PMD) covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. |
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PRINTS |
A compendium of protein fingerprints from (Manchester University) |
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ProDom |
The Protein Domain database. |
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PROSITE |
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. |
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Protein Data Bank |
Worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. |
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Protein Data Bank (PDB) |
Protein database |
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Protein Databases |
Proteins, also known as the essential building blocks of a human body are a vital part of living organisms. Studies regarding the structure and... |
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Protein Information Resource |
Georgetown University Medical Center [GUMC]) |
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Retrieve/ID mapping |
Batch search with UniProt IDs or convert them to another type of database ID (or vice versa) |
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Structural Classification of Proteins (SCOP) |
Structural classification |
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Swiss-model |
Server and repository for protein structure models |
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Swiss-Prot |
Protein knowledgebase (Swiss Institute of Bioinformatics) |
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Text Search |
Search by the name of protein |
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thebiogrid.org |
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. The index searches publications for protein and genetic interactions, chemical associations and post translational modifications from major model organism species. |
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UniProt uniprot.org |
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. |
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unihi.org |
Users can enter gene or protein identifiers from different organisms to obtain physical and regulatory interaction partners in the human interactome. |
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Uniprot |
UniProt Knowledgebase |
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UniprotKB |
UniProt Knowledgebase |
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UnifRef |
Provides clustered sets of sequences |
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UniParc |
A comprehensive and non-redundant database of publicly available protein sequences |
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Variant Effect Predictor |
Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool |
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Variant Recoder |
Translate a variant identifier, HGVS notation or genomic SPDI notation to all possible variant IDs, HGVS, VCF format and genomic SPDI |
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VCF to PED converter |
Parse a vcf file to create a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview |
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wwpdb.org |
Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. |
