| Name | Description | Category |
| PDB | Protein Data Bank (PDB) is a archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. | Structure Summary |
| ProteoPedia | Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules. The site contains a page for every entry in the PDB. | 3D interactive encyclopedia of proteins |
| EBI's EB-eye | The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute | protein structure/function |
| OCA | OCA integrates data from several sources, it allows the user to rapidly search through the contents of the entire PDB Archive for entries obeying certain constraints. | protein structure/function |
| TOPSAN | The Open Protein Structure Annotation Network (TOPSCAN) is a novel way to collect, share and distribute information about protein 3D structures and give knowledge about functions and roles of these proteins in their respective organisms. | protein 3D structures |
| PDBsum | PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. | Structure Summary |
| EDS | The Uppsala Electron Density Server (EDS) provides the scientific community with a service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. | evaluating the electron density of crystal structures |
| PDBe | Protein Data Bank in Europe (PDBe) is the the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB). | Structure Summary |
| PDB REDO | PDB REDO is the method for automated re-refinement of structure models in the PDB. | macromolecular X-ray diffraction structure models |
| PDBwiki | PDBWiki is a user contributed database of protein structure annotations, listing all the protein structures currently available in the PDB. | Structure Summary |
| Procheck | PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. | stereochemical analysis |
| PDBREPORT | The PDBREPORT is a database of observed anomalies in PDB files. PDBREPORT entries can be seen as error reports for macromolecular structures deposited in the PDB. | describing structural problems in PDB entries |
| LPC | Ligand Protein Contact (LPC) is a software which gives detailed analysis of interatomic contacts,calculate the solvent-accessible surface of every atom,determine the contacting residues and type of interaction. | Structure Features |
| CSU | Contacts of Structural Units (CSU) is a tools which describe the contacts of structural units such as helices, sheets, strands and residues. | Structure Features |
| CASTp | Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. | Structure Features |
| GNM | Guassian Network Model (GNM) is a web-based system that describing high-throughput analysis of the collective dynamics of proteins. | Visualizing |
| Chem-BLAST | Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) is a chemical taxonomy-based search engine which search on the fragments of an inhibitor to look for its chemical structural neighbors. | Ligand Features |
| PubChem | PubChem is a database of chemical molecules which is maintained by the NCBI. PubChem provides information on the biological activities of small molecules. | Ligand Features |
| SCOP | Structural Classification of Proteins (SCOP) is a structural classification of proteins database, provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. | Structure Classification |
| CATH | Protein Structure Classification (CATH) is a semi-automatic, hierarchical classification of protein domains. The four main levels of this classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). | Structure Classification |
| VAST | Vector Alignment Search Tool (VAST) is NCBI's structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure. | Structure Classification and Comparison |
| FATCAT | Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) is a flexible protein structure comparison algorithm, which automatically identifies hinges and internal rearrangements in two protein structures. | Structure Alignment and Comparison |
| DSSP | Dictionary of protein secondary structure (DSSP) is a program o standardize secondary structure assignment. | Secondary Structure |
| CSA | The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. | enzyme active sites |
| PDB chain identifiers | PDB chain identifiers is identify the chain is specified in the PDB file. | PDB chain identifier |
| fireDB | fireDB is a database of PDB structures and their associated ligands. fireDB also contains the largest set of reliably annotated functionally important residues. | Functional annotation |
| PDB File | Download PDB file. | PDB file |
| Sequence | Download fasta sequence. | fasta sequence |
| Ramachandran plot of 2pdt | The Ramachandran plot shows the phi-psi torsion angles for all residues in the structure (except those at the chain termini). | Ramachandran plot |
| SCOPOI | SCOPPI (Structural Classification of Protein-Protein Interfaces) is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. | Protein-Protein Interfaces |
| DIP | Datbase of Interacting Proteins (DIP) is a database of experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. | protein-protein interactions |
| SRS link at EBI | SRS is a proven and scalable data integration platform that is used at over 300 commercial and academic sites delivering genomic data to thousands of users. | data integration platform |
| MMDB | Molecular Modeling Database (MMDB) is a database of experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, links to literature, similar sequences, related 3D structures, information about chemicals bound to the structures, and more. | Structure Summary |
| FSSP | Families of structurally similar proteins (FSSP) is a database of structural alignments of proteins in the Protein Data Bank (PDB). | structural alignments |
| PQS | Protein Quaternary Structure server (PQS) is a server allows for searching of the list of likely quaternary structures generated at the EBI. The system is a SQL front end to a database on characteristics of the quaternary structure files. | Protein Quaternary Structure |
| ProSAT | Protein Structure Annotation Tool (ProSAT) is a tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein | 3D structure |
| AffinDB | AffinDB is a affinity database For Protein-Ligand Complexes. | Binding Affinity |
| PDBj | PDBj (Protein Data Bank Japan) maintains a centralized archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. | Structure/Function summary |
| PISA | Protein Interfaces, Surfaces and Assemblies (PISA) is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies | Protein Interfaces, Surfaces |
| JenaLib | The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. | Visualization and analysis |
| PDBCartoon | PDB Cartoon produces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons. | Visualization |
| XDom | A Graphical Tool for Protein Domain and Exon Position Visualization (XDom). | Domain Information |
| WebMol | Complete Structure Visualization | Visualization |
| Jena3D | Complete Structure Visualization | Visualization |
