| 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. BindingMOAD.org closed on July 1, 2024 |
| 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 |
| DNATCO | Enables an in-depth analysis and validation of nucleic acid structures |
| 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. |
| LIPID MAPS® | The LIPID MAPS® Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. |
| 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 |
| 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. |
| 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. |
