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...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Jean-François Taly, Antoine Marin, Jean-François Gibrat
• Keywords: BMCBI 2008, Conformational Space, Native Structure, Protein