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Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

Title
Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
Authors
Lazim, RaudahSuh, DonghyukChoi, Sun
Ewha Authors
최선Siti Raudah Mohamed Lazim
SCOPUS Author ID
최선scopus; Siti Raudah Mohamed Lazimscopus
Issue Date
2020
Journal Title
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN
1422-0067JCR Link
Citation
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES vol. 21, no. 17
Keywords
molecular dynamics simulationenhanced samplingprotein-protein interactionsbinding free energyprotein-ligand binding affinity
Publisher
MDPI
Indexed
SCIE; SCOPUS WOS scopus
Document Type
Review
Abstract
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.
DOI
10.3390/ijms21176339
Appears in Collections:
약학대학 > 약학과 > Journal papers
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