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

Chitrak Gupta; Daipayan Sarkar; D Peter Tieleman; Abhishek Singharoy

doi:10.1016/j.sbi.2022.102338

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

Curr Opin Struct Biol. 2022 Apr:73:102338. doi: 10.1016/j.sbi.2022.102338. Epub 2022 Mar 1.

Authors

Chitrak Gupta¹, Daipayan Sarkar², D Peter Tieleman³, Abhishek Singharoy⁴

Affiliations

¹ School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; Biodesign Institute, Tempe, AZ, 85281, USA. Electronic address: https://twitter.com/ChitrakGupta2.
² School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824-1319, USA. Electronic address: https://twitter.com/17Dsarkar.
³ Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada. Electronic address: [email protected].
⁴ School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; Biodesign Institute, Tempe, AZ, 85281, USA. Electronic address: [email protected].

PMID: 35245737
DOI: 10.1016/j.sbi.2022.102338

Abstract

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 upcoming 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.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Computer Simulation*
Models, Molecular