CABS-flex predictions of protein flexibility compared with NMR ensembles
نویسندگان
چکیده
منابع مشابه
CABS-flex predictions of protein flexibility compared with NMR ensembles
MOTIVATION Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-f...
متن کاملCABS-flex 2.0: a web server for fast simulations of flexibility of protein structures
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we p...
متن کاملCABS-flex: server for fast simulation of protein structure fluctuations
The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular d...
متن کاملAccuracy of protein flexibility predictions.
Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Sch...
متن کاملPredictions of protein flexibility: first-order measures.
The normal modes of a molecule are utilized, in conjunction with classical conformal vector field theory, to define a function that measures the capability of the molecule to deform at each of its residues. An efficient algorithm is presented to calculate the local chain deformability from the set of normal modes of vibration. This is done by considering each mode as an off-grid sample of a def...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btu184