WHAT IF - Revision history

Christoph: /* External links */

2012-07-13T00:05:33Z

‎External links

Christoph at 00:04, 13 July 2012

2012-07-13T00:04:32Z

Christoph: /* See also */

2008-06-24T18:16:50Z

‎See also

Christoph at 18:10, 24 June 2008

2008-06-24T18:10:49Z

Christoph at 18:07, 24 June 2008

2008-06-24T18:07:59Z

New page

'''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, drug]]s, ions, water); and
*interactive manipulation of macromolecules

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.

==References==
<div class="references-small">
* 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, <i>et al.</I>, (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.
</div>

==External links==
*[http://swift.cmbi.ru.nl/whatif/ WHAT IF]
*[http://swift.cmbi.ru.nl/servers/html/index.html free servers]

[[Category:Bioinformatics]]

← Older revision		Revision as of 00:05, 13 July 2012
Line 48:		Line 48:

	[[Category:Bioinformatics]]		[[Category:Bioinformatics]]
−	[[Category:~~X-ray crystallography~~]]	+	[[Category:Crystallography]]

@@ Line 36: / Line 36: @@
 ==See also==
 *[[wikipedia:Category:Molecular modelling software]]
 ==External links==

@@ Line 1: / Line 1: @@
 '''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;
+*[[Homology modeling|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, drug]]s, ions, water); and
+*visualisation of macromolecules and their interaction partners (lipids, drugs, ions, water); and
 *interactive manipulation of macromolecules
 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.
 ==References==
@@ Line 33: / Line 42: @@
 * 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.
 </div>
 ==External links==
@@ Line 47: / Line 48: @@
 [[Category:Bioinformatics]]