Databases

Access user-submitted suggestions of websites related to macromolecular structure.

ABG Directory of 3D structures of antibodies
AfCS-Nature Signaling Gateway Comprehensive resource for information on cell signaling, including facts about the proteins involved in that process
Aquaria-COVID Resource Structural Coverage Map
Binding MOAD A subset of the PDB, containing every high-quality example of ligand-protein binding. Binding MOAD's goal is to be the largest collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature.
BindingDB Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
BMCD Biological Macromolecule Crystallization
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.
Covid-19.bioreproducibility.org Validated models of CoV-2 proteins are available in a dedicated, publicly accessible web service
DashPDB Mac OS X Dashboard widget that accesses PDB data files from RCSB PDB
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.
Human Mitochondrial Protein Database Comprehensive data compiled from various resources on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function
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
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.
Membrane Protein Data Bank A relational database with select structural and functional information on membrane proteins and peptides
MEROPS Peptidase Database
NDB Nucleic Acid Database
OCA A browser-database for structure/function
PDB at a Glance Classification of the structures in the PDB
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 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
RELIBase Structural data about receptor/ligand complexes
UniProtKB A comprehensive, high-quality, and freely accessible resource of protein sequence and functional information.
Zinc A free database of commercially-available compounds for virtual screening.


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Last updated: 9/6/2022