International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 21.3, p. 521   | 1 | 2 |

Section 21.3.3.2.  WHAT IF

O. Dym,a D. Eisenbergb* and T. O. Yeatesc

aUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, UCLA, Box 951570, Los Angeles, CA 90095-1570, USA, bUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry, Molecular Biology Institute and Department of Biological Chemistry, UCLA, Los Angeles, CA 90095-1570, USA, and  cUCLA–DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry & Biochemistry and Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1569, USA
Correspondence e-mail:  david@mbi.ucla.edu

21.3.3.2. WHAT IF

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The molecular modelling and drug design program WHAT IF (Vriend, 1990[link]) performs a large number of geometrical checks, comparing a proposed protein model to a set of canonical distances and angles. These parameters include bond lengths and bond angles, side-chain planarity, torsion angles, interatomic distances, unusual backbone conformations and the Ramachandran plot. New additions (Vriend & Sander, 1993[link]) include a `quality factor', and a number of checks for clashes between symmetry-related molecules. Starting from the hypothesis that atom–atom interactions are the primary determinant of protein folding, the program tests a protein model for proper packing by calculating a contact quality index. Each contact is characterized by its fragment type (80 types from the 20 residues), the atom type and the three-dimensional location of the atom relative to the local frame of the fragment. Sets of database-derived distributions are compared with the actual distribution in the protein model being tested. A good agreement with the database distribution produces a high contact quality index. A low packing score can indicate any of: poor packing, misthreading of the sequence, bad crystal contacts, bad contacts with a co-factor, or proximity to a vacant active site. The contact analysis available in WHAT IF can be used as an independent quality indicator during crystallographic refinement, or during the process of protein modelling and design.

References

Vriend, G. (1990). WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics, 8, 52–56.Google Scholar
Vriend, G. & Sander, C. (1993). Quality control of protein models: directional atomic contact analysis. J. Appl. Cryst. 26, 47–60.Google Scholar








































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