Protein Structure Servers
The Primary Database
  1. The World Wide Protein Data Bank (www.wwpdb.org): access to all published, empirical macromolecular 3D structure data.
Examples of Derived Databases
  1. Proteopedia.Org: All PDB entries in Jmol. Ligands and sites. A wiki with scene-authoring tools.
  2. Evolutionarily conserved patches on protein surfaces (ConSurfDB & ConSurf)
  3. Probable quaternary structure: Specific oligomer/biological assembly coordinates/prediction (MakeMultimer, PISA).
  4. Finding energetically significant cation-pi interactions (CaPTURE Server).
  5. Discovering similar structures without reference to sequences (Dali, FATCAT, VAST, Others).
  6. Model quality by atomic contact analysis: "clashscore" after adding all hydrogen atoms (MolProbity).
  7. Structure prediction by homology/comparative modeling using empirical templates (Swiss Model).
  8. Lipid bilayer boundaries for integral membrane proteins, modeled and visualized by (Orientations of Proteins in Membranes).

    and many, many more not listed here.

by Eric Martz, University of Massachusetts, October 2004. This page updated April 2012; March 2015; June 2017.