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 available for in-house use, or as free servers. Its best known use has been the detection of many millions (often small, but sometimes catastrophic) errors in PDB files.
- 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.