Databases and Knowledgebases

Access additional resources of interest, submitted by community members.

Aquaria-COVID Resource Structural Coverage Map
BindingDB Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
BindingMOAD Binding MOAD is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The website was closed down on July 1st
BMCD Biological Macromolecule Crystallization Database
BRENDA The Comprehensive Enzyme Information System
CAZy Carbohydrate-Active enZYmes
CCDC Cambridge Crystallographic Data Centre (small molecules)
Coronavirus Structural Task Force The Coronavirus Structural Task Force examines the structures from SARS and SARS-CoV-2 which are released to evaluate the quality and improve the structures where possible.
CoSSMos RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database. This tool allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric internal loops, hairpin loops, and bulge loops. Validated models of CoV-2 proteins are available in a dedicated, publicly accessible web service
Crystallography Open Database (COD) Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymer
CXIDB Coherent X-ray Imaging Data Bank for data from Coherent X-ray Imaging (CXI) experiments
Database of Macromolecular Movements Describes the motions that occur in proteins and other macromolecules, particularly using movies
EM DataBank The unified data resource for CryoEM
Entrez NCBI databases
ENZYME Enzyme Nomenclature
ExPASy Molecular Biology server
GenBank Nucleotide sequences
GeneCards Database on human genes, proteins and diseases
GlyCosmos A web portal aiming to integrate the glycosciences with the life sciences about genes, proteins, lipids, pathways and diseases.
GlyGen A data integration and dissemination resource for carbohydrate and glycoconjugate related data which provides computational and informatics resources and tools for glycosciences research.
GlyTouCan An international glycan structure repository with unique accession code for each unique glycan.
IEDB The Immune Epitope Database contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.
IMGT International ImMunoGeneTics Database
KBase Enables users to analyze, share, and collaborate using data and tools designed to help build increasingly realistic models for biological function.
LS-SNP A web tool for genome-wide annotation of human SNPs. The current version, LS-SNP/PDB, provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function.
MEROPS Peptidase Database
NAKB Nucleic Acid Knowledgebase
OCA A browser-database for structure/function
PDBbind Collecting experimentally determined binding affinity data exclusively for all types of biomolecular complexes in the Protein Data Bank, including protein-small molecule, nucleic acid-small molecule, protein-protein, and protein-nucleic acid complexes.
PDBLite Simple PDB search for students and educators
Pfam The Pfam database (hosted by InterPro) is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.
ProNIT Thermodynamic Database for Protein-Nucleic Acid Interactions
Proteopedia Collaborative 3D encyclopedia of proteins and other molecules
ProTherm Thermodynamic Database for Proteins and Mutants
SASBDB Curated repository for small angle scattering data and models.
UniProtKB A comprehensive, high-quality, and freely accessible resource of protein sequence and functional information.
XRDa Xtal Raw Data Archive for raw X-ray diffraction images corresponding to PDB entries
Zinc A free database of commercially-available compounds for virtual screening.

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Last updated: 7/11/2024