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 |
| Biology Workbench | A web resource for searching protein and nucleic acid sequence databases, integrated with access to a variety of analysis and modeling tools |
| 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 |
| CE | Download and run the Java version of the Combinatorial Extension (CE) Algorithm. |
| 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. |
| 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 |
| HIC-Up | Hetero-compound Information |
| HOMSTRAD | Homologous Structure Alignment Database |
| IC50 Calculator | Free IC50 calculator and Computer Aided Drug Design tools and services |
| Jena Image Library of Biological Macromolecules | |
| Jena Image Library Site Database | 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 |
| Molecules To Go | Combines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure. |
| MONSTER | Database for inferring potentially stabilizing non-bonding interactions |
| Morphology of Protein-Protein Interfaces | A visual survey of protein-protein interfaces in homodimeric proteins from the PDB |
| 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 |
| OLDERADO | On Line Database of Ensemble Representative And DOmains |
| 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 |
| PDB_Select | Representative PDB structures |
| PINTS | Patterns in Non-homologous Tertiary Structure - detects similar spatial arrangements of amino acids in protein |
| PINUP | Protein binding site prediction with an empirical scoring function |
| 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 |
| Protein Sidechain Webpage | Information on sidechain conformational analysis, sidechain rotamer libraries, and sidechain conformation prediction |
| PyPDB | A lightweight Python library for algorithmically performing advanced searches of the RCSB Protein Data Bank. |
| Resmap | Automated representation of macromolecular interfaces as two-dimensional networks |
| SCOP | Structural Classification of Proteins (UK), mirrored around the world |
| SCOR | Structural Classification Of RNA |
| SPPIDER | Solvent accessibility based Protein-Protein Interface iDEntification and Recognition |
| STAP | NMR Structure Database refined based on Statistical Torsional Angles Potentials |
| 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 |
| TOPS++FATCAT | Rapid structure database searches |
Please report any encountered broken links to info@rcsb.org
Last updated: 10/14/2021
