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.
See also
External links
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.