The ugly,bad, and good stories of large-scale biomolecular simulations |
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| Affiliation: | 1. School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA;2. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824-1319, USA;3. Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;4. Biodesign Institute, Tempe, AZ, 85281, USA;1. RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;2. RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;3. Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan;4. RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;1. RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;2. RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;3. Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, Wako-shi 351-0198, Japan;4. Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States;1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;2. Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany;3. J. Craig Venter Institute, La Jolla, CA 92037, USA;4. NSF Center for the Physics of Living Cells, Urbana, IL 61801, USA;5. NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA |
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| 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. |
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