WHAT IF software

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WHAT IF is a computer program used in a wide variety of in silico macromolecular structure research fields. The software provides a flexible environment for displaying, manipulating, and analyzing small molecules, proteins, nucleic acids, and their interactions.[1][2]

History[edit]

The first version of the WHAT IF software was developed by Gert Vriend in 1987 at the University of Groningen.[2] Most of its development took place in the period 1989-2000 at the European Molecular Biology Laboratory in Heidelberg. Additional contributors include Chris Sander and Wolfgang Kabsch.[3] The software is currently maintained by the Vriend group at the Dutch Center for Molecular and Biomolecular Informatics in Nijmegen. It is available for in-house use, or as a web-based resource.[4] As of 2015, the original paper describing WHAT IF has been cited more than 3,000 times.

Software[edit]

WHAT IF provides a flexible environment for displaying, manipulating, and analyzing small molecules, proteins, nucleic acids, and their interactions. One significant use of WHAT IF has been the detection of many millions (often small, but sometimes catastrophic) errors in Protein Data Bank (PDB) files.[5] WHAT IF also provides an environment for: homology modeling of protein tertiary structures as well as quaternary structures; the validation of protein structures, notably those deposited in the PDB; correction of protein structures; the visualisation of macromolecules and their interaction partners (for example, lipids, drugs, ions and water) and the interactive manipulation of macromolecules.

WHAT IF is compatible with a number of other bioinformatics software packages, including YASARA and Jmol.[1]

See also[edit]

External links[edit]

References[edit]

  1. ^ a b "WHAT IF homepage". Retrieved 11 August 2015. 
  2. ^ a b Vriend, G (March 1990). "WHAT IF: a molecular modeling and drug design program.". Journal of molecular graphics 8 (1): 52–6, 29. doi:10.1016/0263-7855(90)80070-v. PMID 2268628. 
  3. ^ "WHAT IF - Who are we". Retrieved 11 August 2015. 
  4. ^ Rodriguez, R; Chinea, G; Lopez, N; Pons, T; Vriend, G (1998). "Homology modeling, model and software evaluation: three related resources.". Bioinformatics (Oxford, England) 14 (6): 523–8. doi:10.1093/bioinformatics/14.6.523. PMID 9694991. 
  5. ^ Hooft, RW; Vriend, G; Sander, C; Abola, EE (23 May 1996). "Errors in protein structures.". Nature 381 (6580): 272. doi:10.1038/381272a0. PMID 8692262.