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BMCBI
2008

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

9 years 11 months ago
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
Background: Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of the polypeptide chain. These simplifications facilitate the exploration of the protein conformational space but do not permit to capture entirely the subtle relationship that exists between the amino acid sequence and its native structure. It has been proposed that physics-based energy functions together with techniques for sampling the conformational space, e.g., Monte Carlo or molecular dynamics (MD) simulations, are better suited to the task of modelling proteins at higher resolutions than those of models obtained with the former type of methods. In this study we monitor different protein structural properties along MD trajectories to discriminate correct from erroneous models. These models are based on the sequence-structure alignments provided by our fold recog...
Jean-François Taly, Antoine Marin, Jean-Fra
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Jean-François Taly, Antoine Marin, Jean-François Gibrat
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