Structure Classification and Analysis

  • 3DNA
    Analysis, reconstruction and visualization of nucleic-acid structures
  • ASAView
    Graphical representation of solvent accessibility
  • The ASTRAL compendium
    Databases and tools useful for analyzing protein structures and their sequences
  • 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
  • ELM
    ELM is a resource for predicting functional sites in eukaryotic proteins.
  • eF-site
    electrostatic-surface of Functional site
  • 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
  • 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
  • PDB_Select
    Representative PDB structures
  • PDBSum
    Summaries and structural analyses of PDB data files
  • 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
  • TOPMATCH
    Pairwise Structure Alignment web site
  • TOPS++FATCAT
    Rapid structure database searches

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