Le 15 nov. 09 à 12:54, Kjeldgaard Morten a écrit :
On 14/11/2009, at 20.17, Miguel Ortiz Lombardia wrote:Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit :On 14/11/2009, at 18.55, Ronald E Stenkamp wrote:The rumblings here at the Univ. of Washington among the computational modelers is that some of their current models might be more representative of protein structures in solution than are the crystal structure models. It may take less than a "couple of decades" for a reduced emphasis on crystallographic studies.Molecular models are the result of numbers emerging from computer programs. The results of such computations do not reflect anything in nature. There's no experimental evidence whatsoever, making modelling a very theoretical -- in my eyes uninteresting -- exercise.For what it's worth, protein molecules in crystal structures, with typically > 50% solvent, are already "in solution" to the extent that protein molecules are ever "in solution" in their natural environment.Hi,I think that strong statements and future foretelling are probably not very useful to a discussion that is indeed interesting and that will be put forward more and more often. Crystal structures are actually models themselves.Yes, but models that can be validated against experimental data. The defining characteristics of computational models is that they (A) are 100% dependent on the algortihm, (B) can't be validated at all.
I don't agree (a) they depend not only on the algorithm(s) but also on the setting of the problem, which is kind of an experiment, call it thought experiment if you want, and (b) they can indeed be validated if they make predictions that can be tested experimentally. Just like our own models. True, we can validate our models against our own data, which makes life easier for us, but our data may prove artifactual to some extent: proteins are most often crystallised very far from physiological conditions, crystal contacts may be misinterpreted as functional interactions, our validation tools may fail to detect errors, etc. Briefly, we need also other data to confront our models to.
Best, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2
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