Literature DB >> 33606945

Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.

Tamar Schlick1,2,3, Stephanie Portillo-Ledesma1, Christopher G Myers1, Lauren Beljak4, Justin Chen4, Sami Dakhel4, Daniel Darling4, Sayak Ghosh4, Joseph Hall4, Mikaeel Jan4, Emily Liang4, Sera Saju4, Mackenzie Vohr4, Chris Wu4, Yifan Xu4, Eva Xue4.   

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.

Entities:  

Keywords:  DNA folding; RNA folding; artificial intelligence; biomolecular dynamics; biomolecular modeling; biomolecular simulation; citizen science projects; machine learning; multiscale modeling; protein folding; structure prediction

Mesh:

Year:  2021        PMID: 33606945      PMCID: PMC8105287          DOI: 10.1146/annurev-biophys-091720-102019

Source DB:  PubMed          Journal:  Annu Rev Biophys        ISSN: 1936-122X            Impact factor:   12.981


  169 in total

1.  Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.

Authors:  Ron O Dror; Hillary F Green; Celine Valant; David W Borhani; James R Valcourt; Albert C Pan; Daniel H Arlow; Meritxell Canals; J Robert Lane; Raphaël Rahmani; Jonathan B Baell; Patrick M Sexton; Arthur Christopoulos; David E Shaw
Journal:  Nature       Date:  2013-10-13       Impact factor: 49.962

2.  Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations.

Authors:  Attilio V Vargiu; Francesca Collu; Robert Schulz; Klaas M Pos; Martin Zacharias; Ulrich Kleinekathöfer; Paolo Ruggerone
Journal:  J Am Chem Soc       Date:  2011-06-27       Impact factor: 15.419

3.  Markov state models of protein misfolding.

Authors:  Anshul Sirur; David De Sancho; Robert B Best
Journal:  J Chem Phys       Date:  2016-02-21       Impact factor: 3.488

Review 4.  The coming of age of de novo protein design.

Authors:  Po-Ssu Huang; Scott E Boyken; David Baker
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

5.  ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins.

Authors:  Dong Song; Wei Wang; Wei Ye; Dingjue Ji; Ray Luo; Hai-Feng Chen
Journal:  Chem Biol Drug Des       Date:  2016-09-19       Impact factor: 2.817

6.  Influence of DNA sequence on the structure of minicircles under torsional stress.

Authors:  Qian Wang; Rossitza N Irobalieva; Wah Chiu; Michael F Schmid; Jonathan M Fogg; Lynn Zechiedrich; B Montgomery Pettitt
Journal:  Nucleic Acids Res       Date:  2017-07-27       Impact factor: 16.971

7.  SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins.

Authors:  Ron O Dror; Thomas J Mildorf; Daniel Hilger; Aashish Manglik; David W Borhani; Daniel H Arlow; Ansgar Philippsen; Nicolas Villanueva; Zhongyu Yang; Michael T Lerch; Wayne L Hubbell; Brian K Kobilka; Roger K Sunahara; David E Shaw
Journal:  Science       Date:  2015-06-19       Impact factor: 47.728

8.  Many-body effect determines the selectivity for Ca2+ and Mg2+ in proteins.

Authors:  Zhifeng Jing; Chengwen Liu; Rui Qi; Pengyu Ren
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-23       Impact factor: 11.205

9.  Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.

Authors:  Tamar Schlick
Journal:  F1000 Biol Rep       Date:  2009-07-08

10.  Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism.

Authors:  Jacob D Durrant; Sarah E Kochanek; Lorenzo Casalino; Pek U Ieong; Abigail C Dommer; Rommie E Amaro
Journal:  ACS Cent Sci       Date:  2020-02-19       Impact factor: 14.553

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  8 in total

1.  Biomolecular modeling thrives in the age of technology.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma
Journal:  Nat Comput Sci       Date:  2021-05-20

2.  Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers.

Authors:  Roy Nassar; Emiliano Brini; Sridip Parui; Cong Liu; Gregory L Dignon; Ken A Dill
Journal:  J Chem Theory Comput       Date:  2022-02-08       Impact factor: 6.578

3.  Finite element modeling of α-helices and tropocollagen molecules referring to spike of SARS-CoV-2.

Authors:  Tomasz Wierzbicki; Yuanli Bai
Journal:  Biophys J       Date:  2022-05-20       Impact factor: 3.699

4.  A MULTISCALE VISION-ILLUSTRATIVE APPLICATIONS FROM BIOLOGY TO ENGINEERING.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma; Mischa Blaszczyk; Luke Dalessandro; Somnath Ghosh; Klaus Hackl; Cale Harnish; Shravan Kotha; Daniel Livescu; Arif Masud; Karel Matouš; Arturo Moyeda; Caglar Oskay; Jacob Fish
Journal:  Int J Multiscale Comput Eng       Date:  2021       Impact factor: 1.508

5.  Searching for Low Probability Opening Events in a DNA Sliding Clamp.

Authors:  Reza Esmaeeli; Benedict Andal; Alberto Perez
Journal:  Life (Basel)       Date:  2022-02-09

Review 6.  Progress in Simulation Studies of Insulin Structure and Function.

Authors:  Biswajit Gorai; Harish Vashisth
Journal:  Front Endocrinol (Lausanne)       Date:  2022-06-20       Impact factor: 6.055

Review 7.  Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery.

Authors:  R N V Krishna Deepak; Ravi Kumar Verma; Yossa Dwi Hartono; Wen Shan Yew; Hao Fan
Journal:  Pharmaceuticals (Basel)       Date:  2021-12-22

Review 8.  Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems.

Authors:  A Sofia F Oliveira; Giovanni Ciccotti; Shozeb Haider; Adrian J Mulholland
Journal:  Eur Phys J B       Date:  2021-07-20       Impact factor: 1.500

  8 in total

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