The ugly, bad, and good stories of large-scale biomolecular simulations

被引：38
作者：
Gupta, Chitrak [1 ,5 ]
Sarkar, Daipayan [1 ,2 ]
Tieleman, D. Peter [3 ,4 ]
Singharoy, Abhishek [1 ,5 ]
机构：
[1] Arizona State Univ, Sch Mol Sci, Ctr Appl Struct Discovery, Tempe, AZ 85282 USA
[2] Michigan State Univ, MSU DOE Plant Res Lab, E Lansing, MI 48824 USA
[3] Univ Calgary, Ctr Mol Simulat, Calgary, AB T2N 1N4, Canada
[4] Univ Calgary, Dept Biol Sci, Calgary, AB T2N 1N4, Canada
[5] Biodesign Inst, Tempe, AZ 85281 USA
来源：
CURRENT OPINION IN STRUCTURAL BIOLOGY | 2022年 / 73卷
基金：
加拿大自然科学与工程研究理事会; 美国国家科学基金会;
关键词：
MOLECULAR-DYNAMICS SIMULATIONS; DETERMINANTS;
D O I：
10.1016/j.sbi.2022.102338
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Molecular modeling of large biomolecular assemblies exemplifies a disruptive area holding both promises and contentions. Propelled by peta and exascale computing, several simulation methodologies have now matured into user-friendly tools that are successfully employed for modeling viruses, membranous nano-constructs, and key pieces of the genetic machinery. We present three unifying biophysical themes that emanate from some of the most recent multi-million atom simulation endeavors. Despite connecting molecular changes with phenotypic outcomes, the quality measures of these simulations remain questionable. We discuss the existing and up-coming strategies for constructing representative ensembles of large systems, how new computing technologies will boost this area, and make a point that integrative modeling guided by experimental data is the future of biomolecular computations.
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页数：10
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