Useful Structural Biology Links

Useful Structural Biology Links

Literature resources


Structural Analysis Tools

  • DALI - Comparison of protein structures in 3D.
  • DaliLite - This is a program for pairwise structure comparison. Compare your structure(first structure) to a reference structure(second structure).
  • MaxSprout - Reconstruction of 3D coordinates from C(alpha) trace.
  • NMR Representatives - Search for NMR elucidated structures in the PDB.
  • PQS - Protein quaternary structure query.
  • PQS-Quick - Quickly retrive protein quaternary structure information from PDB ID code.
  • PROCOGNATE - PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
  • Unpublished Reference Server - Many of the current PDB files contain references to papers which are listed as being unpublished. In some cases, the PDB file has become out of date - the paper has been published - but in others the title "To Be Published" still holds true. Part of the aim of the PDB Clean Up at EBI is to update these references and the first stage in achieving this was to sort out the published from the unpublished.

Databases

  • Virus Structure Resource - STRUBI Fuller Group
  • Structural Biology Software Database
  • PDB - Database of 3-D biological macromolecular structure data
  • Swissprot - protein sequence database
  • Prosite - Database of protein families and domains at Expasy
  • SLoop - Database of Super Secondary Fragments
  • Homstrad - Homologous Structure Alignment Database
  • Campass - Cambridge database of Protein Alignments organised as Structural Superfamilies
  • CATH - a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
  • European Bioinformatics Institute Structure Databases
    • CSA - The Catalytic Site Atlas (CSA) is a resource of catalytic sites and residues identified in enzymes using structural data.
    • DALI is a network service for comparing protein structures in 3D. Protein structure domain dictionary.
    • DSSP - The DSSP database is a database of secondary structure assignments (and much more) for all of the entries in the Protein Data Bank (PDB).
    • FSSP - Fold classification based on structure-structure assignments.
    • HSSP - HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D).
    • MSDchem - The ligand library, a complete chemical description of all the distinct chemical components found within the PDB.
    • MSDlite - Provides easy access to the PDB.
    • MSDtarget - The Target Information Server is a tool for searching and tracking structural genomics targets. These include public domain SG and PDB including pre-released sequences.
    • PDBsum - PDBsum is a pictorial database providing an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB).
    • ProFunc - The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure.
    • RESID - The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
    • Macromolecular Structure Database (MSD) is the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). This includes PDB search tools.
      • EM-Deposition Tool For Electron Microscopy Volume Data
      • EMsearch - A search/retrieval tool for electron microscopy depositions.
      • MSD Services - A complete list and summary of all the tools and services the Macromolecular Structure Database (MSD) group have to offer.
      • MSDfold - Secondary structure matching - Compare protein chains/structures and look for similar ones in the whole PDB archive or among SCOP domains.
      • MSDpro - A java applet tool that allows you to construct complex relational queries on the MSD, without needing to know the arrangement of the data within the database, or the language in which such queries are usually written, SQL.
      • MSDsite - This tool allows the ability to search the active site database based on ligand (eg ATP) or active site (eg CYS CYS CYS CYS) information.

Fold recognition servers

  • Fugue - FUGUE uses environment-based fold profiles that are created from structural alignments. Gap penalties are environment dependent.
  • 3DPSSM - Based on sequence profiles, solvatation potentials and secondary structure.
  • SAMT02 - The query is checked against a library of hidden Markov models. This is NOT a threading technique, it is sequence based.
  • GenTHREADER - Combines profiles and sequence-structure alignments. A neural network-based jury system calculates the final score based on solvation and pair potentials.
  • Metaserver - The structure prediction Meta Server offers a gateway to many high quality fold recognition servers and provides and infrastructure and main interface to several highly reliable consensus methods.

Protein structure & alignment analysis


Homology Modelling Servers

  • MODELLER -homology or comparative modelling of protein three-dimensional structures by satisfaction of spatial restraints
  • SWISS-MODEL - SWISS-MODEL is an automated comparative modelling server
  • SDSC1 - Protein structure homology modeling server (San Diego, USA)
  • 3D-JIGSAW - Automated system for 3D models for proteins (Cancer Research)
  • WHATIF - WHAT IF Web interface: homology modelling, drug docking, electrostatics calculations, structure validation and visualisation.

Ab-initio Modelling

  • RAPPER - Restraint-based protein modelling
  • HMMSTR/Rosetta - Prediction of protein structure from sequence

Predicting protein loops

  • CODA - a combined algorithm for predicting protein loops

Structural Validation Tools

  • Biotech - Biotech validation suite for protein structures.
  • RAMPAGE - Structural validation by assessment of the Ramachandran plot
  • PROCHECK - Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
  • WHATIF - Protein structure analysis program for mutant prediction, structure verification, molecular graphics

Molecular visualization tools


Protein-Protein interaction

  • Protein-Protein Interaction Server - The server is a tool to analyse the protein-protein interface of any protein complex. You can submit the coordinates of a protein structure of your choice and then view tables describing the nature of the protein-protein interface.
  • Atlas of Protein Side-Chain Interactions - A record of the hydrogen bonding patterns of the standard hydrogen bonding groups

"10 Simple Rules" Collection

Written by PLoS Computational Biology Editor-in-Chief Philip E. Bourne, sometimes with collaborators, the "Ten Simple Rules" provide a quick, concentrated guide for mastering some of the professional challenges research scientists face in their careers. Some of these articles include:

Bourne, PE. 2007. "Ten simple rules for making good oral presentations." PLoS Computational Biology, 3 (4).

Erren, TC and PE Bourne. 2007. "Ten simple rules for a good poster presentation." PLoS Computational Biology, 3 (5).

Vicens, Q and PE Bourne. 2007. "Ten simple rules for a successful collaboration." PLoS Computational Biology, 3 (3).

Bourne, PE and LM Chalupa. 2006. "Ten simple rules for getting grants." PLoS Computational Biology, 2 (2).

Bourne, PE and A Korngreen. 2006. "Ten simple rules for reviewers." PLoS Computational Biology, 2 (9).

Bourne, PE and I Friedberg. 2006. "Ten simple rules for selecting a postdoctoral position." PLoS Computational Biology, 2 (11).

Bourne, PE. 2005. "Ten simple rules for getting published." PLoS Computational Biology, 1 (5).