PredyFlexy: flexibility and local structure prediction from sequence. - Inserm - Institut national de la santé et de la recherche médicale Accéder directement au contenu
Article Dans Une Revue Nucleic Acids Research Année : 2012

PredyFlexy: flexibility and local structure prediction from sequence.


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
Fichier principal
Vignette du fichier
nar.gks482.full.pdf (1.64 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

inserm-00750270 , version 1 (09-11-2012)



Alexandre de Brevern, Aurélie Bornot, Pierrick Craveur, Catherine Etchebest, Jean-Christophe Gelly. PredyFlexy: flexibility and local structure prediction from sequence.. Nucleic Acids Research, 2012, 40 (Web Server issue), pp.W317-22. ⟨10.1093/nar/gks482⟩. ⟨inserm-00750270⟩
126 Consultations
163 Téléchargements



Gmail Facebook X LinkedIn More