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Schlick T, Portillo-Ledesma S, Myers CG, Beljak L, Chen J, Dakhel S, Darling D, Ghosh S, Hall J, Jan M, Liang E, Saju S, Vohr M, Wu C, Xu Y, Xue E. Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. Annu Rev Biophys 2021; 50:267-301. [PMID: 33606945 PMCID: PMC8105287 DOI: 10.1146/annurev-biophys-091720-102019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy andscope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, New York 10003, USA;
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | | | - Christopher G Myers
- Department of Chemistry, New York University, New York, New York 10003, USA;
| | - Lauren Beljak
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Justin Chen
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sami Dakhel
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Daniel Darling
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sayak Ghosh
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Joseph Hall
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mikaeel Jan
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Emily Liang
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sera Saju
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mackenzie Vohr
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Chris Wu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Yifan Xu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Eva Xue
- College of Arts and Science, New York University, New York, New York 10003, USA
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Baudry J, Bondar AN, Cournia Z, Parks JM, Petridis L, Roux B. Editorial: Advances in computational molecular biophysics. Biochim Biophys Acta Gen Subj 2021; 1865:129888. [PMID: 33662454 DOI: 10.1016/j.bbagen.2021.129888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Jerome Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences, 301 Sparkman Drive, Huntsville, AL 35899, USA.
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany.
| | - Zoe Cournia
- Soranou Ephessiou, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831-6309, USA.
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831-6309, USA.
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E57th Street, Chicago, IL 60637, USA.
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Abstract
Novel RNA motif design is of great practical importance for technology and medicine. Increasingly, computational design plays an important role in such efforts. Our coarse-grained RAG (RNA-As-Graphs) framework offers strategies for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates. In RAG, RNA secondary structures are represented as tree or dual graphs. Graphs with known RNA structures are called "existing", and the others are labeled "hypothetical". By using simplified features for RNA graphs, we have clustered the hypothetical graphs into "RNA-like" and "non-RNA-like" groups and proposed RNA-like graphs as candidates for design. Here, we propose a new way of designing graph features by using Fiedler vectors. The new features reflect graph shapes better, and they lead to a more clustered organization of existing graphs. We show significant increases in K-means clustering accuracy by using the new features (e.g., up to 95% and 98% accuracy for tree and dual graphs, respectively). In addition, we propose a scoring model for top graph candidate selection. This scoring model allows users to set a threshold for candidates, and it incorporates weighing of existing graphs based on their corresponding number of known RNAs. We include a list of top scored RNA-like candidates, which we hope will stimulate future novel RNA design.
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Affiliation(s)
- Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Tamar Schlick
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P. R. China
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Šulc P. The Multiscale Future of RNA Modeling. Biophys J 2020; 119:1270-1272. [PMID: 32941784 PMCID: PMC7462927 DOI: 10.1016/j.bpj.2020.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona.
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