Additional Resources
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 BindingMOAD.org 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. |
Covid-19.bioreproducibility.org | 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