MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments.
J Chem Theory Comput
; 2023 Jan 09.
Article
em En
| MEDLINE
| ID: mdl-36622950
ABSTRACT
Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions. Herein, we developed a new automated open-source implementation, MDexciteR (https//github.com/mcosta27/MDexciteR), enabling the integration of MDeNM with two commonly used simulation programs with GPU support. Second, we generalized the method to include the excitation of principal components calculated from experimental ensembles. Finally, we evaluated whether the use of coarse-grained normal modes calculated with elastic network representations preserved the performance and accuracy of the method. The advantages and limitations of these new approaches are discussed based on results obtained for three different protein test cases two globular and a protein/membrane system.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
J Chem Theory Comput
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Brasil