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Assemblage flexible de macromolécules : la théorie du champ moyen appliquée au remodelage des boucles protéiques
| Content Provider | Semantic Scholar |
|---|---|
| Author | Bastard, Karine |
| Copyright Year | 2005 |
| Abstract | Docking methods aim to predict the structure of a macromolec ular complex starting from the atomic coordinates of its individual components. Most of these methods do not consider the internal deformations that may occur during association. We propose a novel algorithm to introduce loop flexibility into docking methods. In this algorithm, each fle xible loop is represented by an ensemble of rigid conformations, generated prior to the docking. Fol lowing the principle of the mean-field theory, each conformation is caracterized by a weight, roug hly corresponding to the probability that the loop adopts such conformation for a given position o f the partner. We have introduced this strategy into two docking programs, in each case coupling th e mean-field theory with the exploration methods used by the programs. The first one performs an exhaustive search of all possible partner combinations, based on energy minization, and allo wed by the use of a simplified protein representation. The second program allows to predict the de tails of interaction between the two macromolecules with a Monte-Carlo process bearing on the pa rtner positions within a restricted space. We present preliminar and promising results concern ing the application of our method to model a complex system : the RecA nucleo-protein filament. |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://csb.stanford.edu/karine/thesis-k-bastard.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
