RCSB PDB Help
Additional Resources
Structure Classification and Analysis
Access user-submitted suggestions of websites related to macromolecular structure.
| 3DNA | Analysis, reconstruction and visualization of nucleic-acid structures |
| ASAView | Graphical representation of solvent accessibility |
| CAFASP | Critical Assessment of Fully Automated Structure Prediction servers |
| CASTp | Server that calculates measurements of structural pockets and cavities of proteins and nucleic acids |
| CATH | Class, architecture, topology and homologous superfamily |
| ConSurf | Server for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information |
| DALI | Comparison of protein structures in 3D |
| DNAproDB | an interactive tool for structural analysis of DNA-protein complexes |
| eF-site | electrostatic-surface of Functional site |
| ELM | ELM is a resource for predicting functional sites in eukaryotic proteins. |
| Evolutionary Trace Server | Ranks amino acid residues in a protein sequence by their relative evolutionary importance. |
| FATCAT | Flexible and rigid protein structure comparison. |
| FATCAT | FATCAT - Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists |
| HB Plot | HB plot is a tool for exploring protein structure and function by describing structure as a network of hydrogen bonding interaction. |
| Het-PDB Navi | List of all Het atoms in the PDB, or search by PDB ID or Het code |
| HOMSTRAD | Homologous Structure Alignment Database |
| IC50 Calculator | Free IC50 calculator and Computer Aided Drug Design tools and services |
| Jena Image Library of Biological Macromolecules | Provides information on sites included in three-dimensional biopolymer structures |
| JStruct | JStruct provides a robust and secure means to store, access, search and utilize both public and proprietary structures within the same system. With JStruct it is possible to search, calculate and compare structures across a full set of files while keeping internal sequences from being publicly exposed. |
| MAMMOTH | MAtching Molecular Models Obtained from THeory - a program for automated pairwise and multiple structural alignments; for SGI, Linux, and Sun Solaris |
| Multiple Interface String Alignment (MISA) | Tool to display coherently various sequence and structure-based statistics at protein-protein interfaces |
| nightshift | Python command line utility and library for plotting simulated 2D and 3D NMR spectra from assigned chemical shifts in the BMRB |
| Non-covalent bond finder | Software for finding non-covalent interactions for use with Chime 2 or higher |
| PALI | Phylogeny and ALIgnment of homologous protein structures |
| PartsList | Dynamic protein fold ranking by disparate attributes, including whole-genome expression and interaction information |
| PDBe | PDBe database and search tools |
| PDBSum | Summaries and structural analyses of PDB data files |
| PISCES | A protein sequence culling server - representative PDB structures |
| ProBiS | A freely available web server for protein binding sites prediction. |
| ProFit | A program for fitting protein structures on to each other |
| PyPDB | A lightweight Python library for algorithmically performing advanced searches of the RCSB Protein Data Bank. |
| RC-Hydrolase | RC-Hydrolase is a database for three-dimensional structural data of catalytic/reactive centers of single and multi-chain enzyme molecules listed in the Protein Data Bank (PDB) |
| Resmap | Automated representation of macromolecular interfaces as two-dimensional networks |
| SCOR | Structural Classification Of RNA |
| SPPIDER | Solvent accessibility based Protein-Protein Interface iDEntification and Recognition |
| Surface Racer | A program that calculates exact accessible surface area, molecular surface area and average curvature of molecular surface, and analyzes cavities in the protein interior inaccessible from the outside. |
| SURFNET | A program which generates surfaces and void regions between molecular surfaces |
| SWISS-MODEL | A server for automated protein modeling |
| The ASTRAL compendium | Databases and tools useful for analyzing protein structures and their sequences |
| TOPMATCH | Pairwise Structure Alignment web site |
Please report any encountered broken links to info@rcsb.org
Last updated: 8/8/2024
