Additional Resources
Databases and Knowledgebases
Access additional resources of interest, submitted by community members.
| 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 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: 2/28/2024
