An approximate method in using molecular mechanics simulations to study slow protein conformational changes
Article Abstract:
An approximate method that employs the standard molecular dynamics simulations is described to study and explain the structural, as well as conformational changes for slow systematic motions of large complex systems of proteins. The results show that though the method breaks the original detailed balance of the system, the intermediate conformations can still be used for the identification of the reaction coordinates of such systems.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Metadynamics in essential coordinates: Free energy simulation of conformational changes
Article Abstract:
A method that integrates an extraction of collective motions of a molecular system with a sampling of its free energy surface is presented, where the technique unites an effective sampling and a self-healing nature of metadynamics along with a common dimensionality reduction method. The combination of metadynamics and essential dynamics has provided great opportunities in research of conformational changes in peptides and proteins.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Molecular dynamics simulation of the Ala-pro dipeptide in water: conformational dynamics of trans and Cis isomers using different water models
Article Abstract:
Molecular dynamics simulations of a single dipeptide (Ala-Pro) molecule in water were carried out unsung different water models, the modified TIP3P, the refined SPC, and the original SPC/E. The hydration of the dipeptide was found to depend both on its conformation and on the water model.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2001
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