Structure Classification and Analysis

Access user-submitted suggestions of websites related to macromolecular structure.

3DNAAnalysis, reconstruction and visualization of nucleic-acid structures
ASAViewGraphical representation of solvent accessibility
Biology WorkbenchA web resource for searching protein and nucleic acid sequence databases, integrated with access to a variety of analysis and modeling tools
CAFASPCritical Assessment of Fully Automated Structure Prediction servers
CASTpServer that calculates measurements of structural pockets and cavities of proteins and nucleic acids
CATHClass, architecture, topology and homologous superfamily
CEDownload and run the Java version of the Combinatorial Extension (CE) Algorithm.
ConSurfServer for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
DALIComparison of protein structures in 3D
DNAproDBan interactive tool for structural analysis of DNA-protein complexes
eF-siteelectrostatic-surface of Functional site
ELMELM is a resource for predicting functional sites in eukaryotic proteins.
Evolutionary Trace ServerRanks amino acid residues in a protein sequence by their relative evolutionary importance.
FATCATFlexible and rigid protein structure comparison.
HB PlotHB plot is a tool for exploring protein structure and function by describing structure as a network of hydrogen bonding interaction.
Het-PDB NaviList of all Het atoms in the PDB, or search by PDB ID or Het code
HIC-UpHetero-compound Information
HOMSTRADHomologous Structure Alignment Database
IC50 CalculatorFree IC50 calculator and Computer Aided Drug Design tools and services
Jena Image Library of Biological Macromolecules
Jena Image Library Site DatabaseProvides information on sites included in three-dimensional biopolymer structures
JStructJStruct 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.
MAMMOTHMAtching Molecular Models Obtained from THeory - a program for automated pairwise and multiple structural alignments; for SGI, Linux, and Sun Solaris
Molecules To GoCombines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure.
MONSTERDatabase for inferring potentially stabilizing non-bonding interactions
Morphology of Protein-Protein InterfacesA 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 finderSoftware for finding non-covalent interactions for use with Chime 2 or higher
OLDERADOOn Line Database of Ensemble Representative And DOmains
PALIPhylogeny and ALIgnment of homologous protein structures
PartsListDynamic protein fold ranking by disparate attributes, including whole-genome expression and interaction information
PDBePDBe database and search tools
PDBSumSummaries and structural analyses of PDB data files
PDB_SelectRepresentative PDB structures
PINTSPatterns in Non-homologous Tertiary Structure - detects similar spatial arrangements of amino acids in protein
PINUPProtein binding site prediction with an empirical scoring function
PISCESA protein sequence culling server - representative PDB structures
ProBiSA freely available web server for protein binding sites prediction.
ProFitA program for fitting protein structures on to each other
Protein Sidechain WebpageInformation on sidechain conformational analysis, sidechain rotamer libraries, and sidechain conformation prediction
PyPDBA lightweight Python library for algorithmically performing advanced searches of the RCSB Protein Data Bank.
ResmapAutomated representation of macromolecular interfaces as two-dimensional networks
SCOPStructural Classification of Proteins (UK), mirrored around the world
SCORStructural Classification Of RNA
SPPIDERSolvent accessibility based Protein-Protein Interface iDEntification and Recognition
STAPNMR Structure Database refined based on Statistical Torsional Angles Potentials
Surface RacerA 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.
SURFNETA program which generates surfaces and void regions between molecular surfaces
SWISS-MODELA server for automated protein modeling
The ASTRAL compendiumDatabases and tools useful for analyzing protein structures and their sequences
TOPMATCHPairwise Structure Alignment web site
TOPS++FATCATRapid structure database searches

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Last updated: 10/14/2021