Structure Analysis and Verification

• CE/CL
  Software for structure comparison by Combinatorial Extension (CE) and Compound Likeness (CL)
• ENDscript
  A Web server for searching homologous sequences and giving information on secondary structure elements, accessibility, hydropathy and protein-protein contacts
• ESPript
  Easy Sequencing in Postscript
   
• Non-covalent bond finder
  Software for finding non-covalent interactions for use with Chime 2 or higher
• PASS
  A fast cavity-detection program for the identification and visualization of possible protein binding sites
• Procheck
  A program that checks the stereochemical quality of a protein structure
• ProFit
  A program for fitting protein structures on to each other
• SARF2
  A program which searches for similar structural motifs (via an analysis of backbone fragments) in protein structures

• STRAP
  Structural Alignment Program for Proteins, interactive extendable and scriptable editor for large protein alignments which integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence; Windows, Mac OSX, Unix, Linux
   
• 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
• WHAT_CHECK
  A system for protein structure validation derived from the WHAT IF program
• WHAT IF
  A protein structure analysis program that may be used for mutant prediction, structure verification and molecular graphics