Format

Send to

Choose Destination
See comment in PubMed Commons below
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W317-22. doi: 10.1093/nar/gks482. Epub 2012 Jun 11.

PredyFlexy: flexibility and local structure prediction from sequence.

Author information

1
INSERM, U665, DSIMB, Paris, France. alexandre.debrevern@univ-paris-diderot.fr

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/.

PMID:
22689641
PMCID:
PMC3394303
DOI:
10.1093/nar/gks482
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center