WHAT IF software

WHAT IF is a computer program used in a wide variety of "in silico" macromolecular structure research fields such as:
* Homology models of protein tertiary structures as well as quaternary structures,
* Validation of protein structures, noticeably those deposited in the PDB
* Correction of protein structures
* Visualisation of macromolecules and their interaction partners (lipids, drugs, ions, water).
* Interactive manipulation of macromolecules

The software was initiated in 1987 at the University of Groningen. Most of its development took place in the period 1989-2000 at the EMBL in Heidelberg. Lately the software is being maintained at the CMBI in Nijmegen. It is [http://swift.cmbi.ru.nl/whatif/ available] for in-house use, or as [http://swift.cmbi.ru.nl/ free servers] . Its best known use has been the detection of many millions (often small, but sometimes catastrophic) [http://swift.cmbi.ru.nl/gv/pdbreport/ errors] in PDB files.

External links

* [http://swift.cmbi.ru.nl/whatif/ WHAT IF]

References

* G. Vriend, (1990). WHAT IF: A molecular modeling and drug design program. "J. Mol. Graph." 8, 52-56.
* G. Vriend, (1990). Parameter relation rows: a query system for protein structure function relationships. "Prot. Engin." 4, 221-223.
* G. Vriend, C. Sander, (1991). Detection of common three-dimensional substructures in proteins. "PROTEINS" 11, 52-58.
* G. Vriend, C. Sander. (1993). Quality control of protein models: Directional atomic contact analysis. "J. Appl. Cryst." 26, 47-60.
* V. de Filippis, C. Sander, G. Vriend, (1994). Predicting local structural changes that result from point mutations. "Prot. Engin." 7, 1203-1208.
* G. Vriend, C. Sander, P.F.W. Stouten, (1994). A novel search method for protein sequence-structure relations, using property profiles. "Prot. Engin." 7, 23-29.
* R. Hooft, C. Sander, G. Vriend, (1994). Reconstruction of symmetry related molecules from protein data bank (PDB) files. "J. Appl. Cryst." 27, 1006-1009.
* G. Chinea, G. Padron, R.W.W.Hooft, C.Sander, G.Vriend, (1995). The use of position specific rotamers in model building by homology. "PROTEINS" 23, 415-421.
* R.W.W.Hooft, C.Sander, G.Vriend, (1996). Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. "PROTEINS" 26, 363-376.
* R.W.W. Hooft, G. Vriend, C. Sander, E.E. Abola, (1996). Errors in protein structures. "Nature" 381, 272-272.
* R.W.W. Hooft, C.Sander and G.Vriend, (1996). Verification of protein structures: Side-chain planarity. "J. Appl. Cryst." 29, 714--716.
* R.W.W. Hooft, C.Sander and G.Vriend, (1997). Objectively judging the quality of a protein structure from a Ramachandran plot. "CABIOS (Now: Bioinformatics)" 13, 425-430.
* K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al., (1998). Who checks the checkers? Four validation tools applied to eight atomic resolution structures. "J. Mol. Biol." 276,417-436.
* R.Rodriguez, G.Chinea, N.Lopez, T.Pons, G.Vriend, (1998). Homollogy modelling, model and software evaluation: three related resources. "Bioinformatics" 14, 523-528.
* J.E. Nielsen, K.V. Andersen, B. Honig, R.W. Hooft, G. Klebe, G. Vriend, R.C. Wade, (1999). Improving macromolecular electrostatics calculations. "Prot. Engin." 12, 657-662.
* Rodriguez R, Chinea G, Lopez N, Vriend G, (1999) Full window stereo. "J. Mol. Graph. & Mod." 17, 310-313.
* Altenberg-Greulich, B., Vriend G., (2001) Where to attach dye molecules to a protein: lessons from WHAT IF. "J. Mol. Struc." 598, 1-8.
* Nielsen, JE., Vriend G. (2001) Optimizing the Hydrogen-Bond Network in Poisson-Boltzmann Equation-based pKa Calculations. "PROTEINS" 43, 403-412.
* Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. (2003) Quantitative evaluation of experimental NMR restraints. "JACS" 2003 125, 12026-12034.
* Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G., (2003) The precision of NMR structure ensembles revisited. "J. Biomol. NMR" 25, 225-234.
* Krieger E, Nabuurs SB, Vriend G. (2003) Homology modeling. "Methods Biochem. Anal." 44, 509-523.
* Nabuurs SB, Spronk CA, Vuister GW, Vriend G. (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. "PLoS Comput. Biol." 2, e9.