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.
Resmap Automated representation of macromolecular interfaces as two-dimensional networks
SCOP Structural Classification of Proteins (UK)
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: 2/23/2023