PredyFlexy: flexibility and local structure prediction from sequence.

Alexandre De Brevern 1, * Aurélie Bornot 2 Pierrick Craveur 2 Catherine Etchebest 2 Jean-Christophe Gelly 2
* Auteur correspondant
1 DSIMB
DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques
2 DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques
Abstract : Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/.
Keywords : Protein Data Bank amino acid structural alphabet Long Structural Prototypes protein folds disorder Support Vector Machines evolutionary information Protein Data Bank.
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Article dans une revue
Nucleic Acids Research, Oxford University Press, 2012, 40 (Web Server issue), pp.W317-22. 〈10.1093/nar/gks482〉
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Alexandre De Brevern, Aurélie Bornot, Pierrick Craveur, Catherine Etchebest, Jean-Christophe Gelly. PredyFlexy: flexibility and local structure prediction from sequence.. Nucleic Acids Research, Oxford University Press, 2012, 40 (Web Server issue), pp.W317-22. 〈10.1093/nar/gks482〉. 〈inserm-00750270〉

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