WHAT IF software

WHAT IF
Original author(s) Gert Vriend, Chris Sander, Wolfgang Kabsch
Developer(s) University of Groningen;
EMBL, Heidelberg;
CMBI, Radboud University Nijmegen;
Radboud University Nijmegen Medical Centre (Radboudumc)
WHAT IF Foundation
Initial release 6 December 1987 (1987-12-06)
Stable release
6.0 / 2016 (2016)
Development status Active
Written in Fortran, C, OpenGL
Operating system Linux
Platform x86
Available in English
Type Molecular modelling
License Proprietary, shareware for academics
Website swift.cmbi.ru.nl/whatif

WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large molecules, proteins, nucleic acids, and their interactions.[1][2]

History

The first version of the WHAT IF software was developed by Gert Vriend in 1987 at the University of Groningen, Groningen, Netherlands.[2] Most of its development occurred during 1989-2000 at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. Other contributors include Chris Sander, and Wolfgang Kabsch.[3] As of 2016, the software is maintained by the Vriend group at the Dutch Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, Netherlands. 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

WHAT IF provides a flexible environment to display, manipulate, and analyze small molecules, proteins, nucleic acids, and their interactions. One notable use was detecting many millions of errors (often small, but sometimes catastrophic) in Protein Data Bank (PDB) files.[5] WHAT IF also provides an environment for: homology modeling of protein tertiary structures and quaternary structures; validating protein structures, notably those deposited in the PDB; correcting protein structures; visualising macromolecules and their interaction partners (for example, lipids, drugs, ions, and water), and manipulating macromolecules interactively.

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

See also

References

  1. 1 2 "WHAT IF homepage". Retrieved 11 August 2015.
  2. 1 2 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.
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