Structure analysis

PROCHECK

Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. The aim of PROCHECK is to assess how normal, or conversely how unusual, the geometry of the residues in a given protein structure is, as compared with stereochemical parameters derived from well-refined, high-resolution structures. The references for PROCHECK are:

Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291.

RA Laskowski, JA Rullmann, MW MacArthur, R Kaptein and JM Thornton. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR (1993) J Biomol NMR. 8, 477-486. Pubmed

Contains a suite of programs (WHAT_CHECK) to assess the "stereochemical quality" of a given protein structure. References for WHATIF and WHAT_CHECK are:

G Vriend. WHAT IF: A molecular modeling and drug design program (1990) J Mol Graph 8, 52-56. Pubmed

RWW Hooft, G Vriend, C Sander and EE Abola. Errors in protein structures (1996) Nature 381, 272-272. Pubmed

PROSA II

Suppose you are confronted with the three-dimensional structure of a protein. The structure may have been determined by X-ray analysis or NMR-spectroscopy, or it may be the result of modeling studies. Prosa II helps you to answer the questions: is the structure correct? are there faulty parts? The reference for PROSA II is:

MJ Sippl. Recognition of errors in three-dimensional structures of proteins (1993) Proteins 17, 355-362. Pubmed