Literature DB >> 21034218

Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems.

Shina C L Kamerlin1, Spyridon Vicatos, Anatoly Dryga, Arieh Warshel.   

Abstract

Recent years have witnessed an explosion in computational power, leading to attempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications. The introduction of such coarse graining can be traced back to the early usage of a simplified model in studies of proteins. Since then, the field has progressed tremendously. In this review, we cover both key developments in the field and potential future directions. Additionally, particular emphasis is given to two general approaches, namely the renormalization and reference potential approaches, which allow one to move back and forth between the coarse-grained (CG) and full models, as these approaches provide the foundation for CG modeling of complex systems.

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Year:  2011        PMID: 21034218     DOI: 10.1146/annurev-physchem-032210-103335

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  56 in total

1.  Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase.

Authors:  Shayantani Mukherjee; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-05       Impact factor: 11.205

2.  Realistic simulation of the activation of voltage-gated ion channels.

Authors:  Anatoly Dryga; Suman Chakrabarty; Spyridon Vicatos; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-13       Impact factor: 11.205

Review 3.  Capturing the essence of folding and functions of biomolecules using coarse-grained models.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Nat Commun       Date:  2011-09-27       Impact factor: 14.919

4.  On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes.

Authors:  Anna Rychkova; Spyridon Vicatos; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

Review 5.  Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development.

Authors:  Dheeraj S Tomar; Sandeep Kumar; Satish K Singh; Sumit Goswami; Li Li
Journal:  MAbs       Date:  2016-01-06       Impact factor: 5.857

6.  Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).

Authors:  Arieh Warshel
Journal:  Angew Chem Int Ed Engl       Date:  2014-07-24       Impact factor: 15.336

7.  Multiscale simulation of microbe structure and dynamics.

Authors:  Harshad Joshi; Abhishek Singharoy; Yuriy V Sereda; Srinath C Cheluvaraja; Peter J Ortoleva
Journal:  Prog Biophys Mol Biol       Date:  2011-07-23       Impact factor: 3.667

8.  Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.

Authors:  Laurence Leherte; Daniel P Vercauteren
Journal:  J Comput Aided Mol Des       Date:  2011-09-14       Impact factor: 3.686

9.  Edgeworth expansions for slow-fast systems with finite time-scale separation.

Authors:  Jeroen Wouters; Georg A Gottwald
Journal:  Proc Math Phys Eng Sci       Date:  2019-03-06       Impact factor: 2.704

10.  Coarse-grained molecular dynamics studies of the structure and stability of peptide-based drug amphiphile filaments.

Authors:  Myungshim Kang; Honggang Cui; Sharon M Loverde
Journal:  Soft Matter       Date:  2017-11-01       Impact factor: 3.679

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