Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
- 주제(키워드) molecular dynamics simulation , enhanced sampling , protein-protein interactions , binding free energy , protein-ligand binding affinity
- 주제(기타) Biochemistry & Molecular Biology
- 주제(기타) Chemistry, Multidisciplinary
- 설명문(일반) [Choi, Sun] Ewha Womans Univ, Coll Pharm, Seoul 03760, South Korea; Ewha Womans Univ, Grad Sch Pharmaceut Sci, Seoul 03760, South Korea
- 등재 SCIE, SCOPUS
- OA유형 Green Published, gold
- 발행기관 MDPI
- 발행년도 2020
- 총서유형 Journal
- URI http://www.dcollection.net/handler/ewha/000000174524
- 본문언어 영어
- Published As http://dx.doi.org/10.3390/ijms21176339
- PubMed https://pubmed.ncbi.nlm.nih.gov/32882859
초록/요약
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.
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