Databases

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

ABGDirectory of 3D structures of antibodies
AfCS-Nature Signaling GatewayComprehensive resource for information on cell signaling, including facts about the proteins involved in that process
Aquaria-COVID ResourceStructural Coverage Map
Binding MOADA 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.
BindingDBDatabase of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
BMCDBiological Macromolecule Crystallization
BRENDAThe Comprehensive Enzyme Information System
CAZyCarbohydrate-Active enZYmes
CCDCCambridge Crystallographic Data Centre (small molecules)
Coronavirus Structural Task ForceThe 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.
CoSSMosRNA 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.orgValidated models of CoV-2 proteins are available in a dedicated, publicly accessible web service
DashPDBMac OS X Dashboard widget that accesses PDB data files from RCSB PDB
Database of Macromolecular MovementsDescribes the motions that occur in proteins and other macromolecules, particularly using movies
EM DataBankThe unified data resource for CryoEM
EntrezNCBI databases
ENZYMEEnzyme Nomenclature
ExPASyMolecular Biology server
GenBankNucleotide sequences
GeneCardsDatabase 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 DatabaseComprehensive data compiled from various resources on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function
IEDBThe Immune Epitope Database contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.
IMGTInternational ImMunoGeneTics Database
LS-SNPA 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 BankA relational database with select structural and functional information on membrane proteins and peptides
MEROPSPeptidase Database
ModBaseA database of comparative protein structure models
NDBNucleic Acid Database
OCAA browser-database for structure/function
PDB at a GlanceClassification of the structures in the PDB
PDBbindCollecting 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.
PDBLiteSimple PDB search for students and educators
PfamThe Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.
ProNITThermodynamic Database for Protein-Nucleic Acid Interactions
ProteopediaCollaborative 3D encyclopedia of proteins and other molecules
ProThermThermodynamic Database for Proteins and Mutants
RELIBaseStructural data about receptor/ligand complexes
SWISS-MODEL RepositoryA database of annotated protein structure homology models
UniProtKBA comprehensive, high-quality, and freely accessible resource of protein sequence and functional information.
ZincA free database of commercially-available compounds for virtual screening.


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Last updated: 1/29/2022