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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
  • 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
  • LPC/CSU
    The LPC/CSU server for analysis of contacts between structural units in proteins and ligand-protein contacts.
  • 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
  • PPI-Pred
    Predicts protein-protein binding sites using a combination of surface patch analysis and a support vector machine (SVM) trained on proteins involved in both obligate and non-obligate interactions.
  • 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
  • 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
  • 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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