Literature DB >> 29477047

New developments in force fields for biomolecular simulations.

Paul S Nerenberg1, Teresa Head-Gordon2.   

Abstract

Biomolecular force field development has been instrumental in improving the predictive power of molecular simulations over the past four decades. More recently, the era of large quantitative experimental datasets and ubiquitous high performance computing power has enabled rapid progress in the field. In this review we summarize recent developments in all-atom protein, nucleic acid, and small molecule force fields, paying specific attention to developments in parameterization methods and improvements in the representations of nonbonded interactions that are critical for solving the challenging biophysical problems of the present. We also sketch out new avenues for force field development and grand challenge applications for the near future.
Copyright © 2018 Elsevier Ltd. All rights reserved.

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Year:  2018        PMID: 29477047     DOI: 10.1016/j.sbi.2018.02.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  35 in total

1.  The combined force field-sampling problem in simulations of disordered amyloid-β peptides.

Authors:  James Lincoff; Sukanya Sasmal; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2019-03-14       Impact factor: 3.488

2.  Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.

Authors:  Petra Kührová; Vojtěch Mlýnský; Marie Zgarbová; Miroslav Krepl; Giovanni Bussi; Robert B Best; Michal Otyepka; Jiří Šponer; Pavel Banáš
Journal:  J Chem Theory Comput       Date:  2019-04-02       Impact factor: 6.006

3.  A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Authors:  Yi Peng; Shufen Cao; Janna Kiselar; Xiangzhu Xiao; Zhanwen Du; An Hsieh; Soobin Ko; Yinghua Chen; Prashansa Agrawal; Wenwei Zheng; Wuxian Shi; Wei Jiang; Lin Yang; Mark R Chance; Witold K Surewicz; Matthias Buck; Sichun Yang
Journal:  Structure       Date:  2018-12-20       Impact factor: 5.006

4.  Data-driven analysis of the number of Lennard-Jones types needed in a force field.

Authors:  Michael Schauperl; Sophie Kantonen; Lee-Ping Wang; Michael K Gilson
Journal:  Commun Chem       Date:  2020-11-13

5.  Ligand binding free-energy calculations with funnel metadynamics.

Authors:  Stefano Raniolo; Vittorio Limongelli
Journal:  Nat Protoc       Date:  2020-08-19       Impact factor: 13.491

6.  Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.

Authors:  Sophie M Kantonen; Hari S Muddana; Michael Schauperl; Niel M Henriksen; Lee-Ping Wang; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2020-01-17       Impact factor: 6.006

7.  Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.

Authors:  Gül H Zerze; Wenwei Zheng; Robert B Best; Jeetain Mittal
Journal:  J Phys Chem Lett       Date:  2019-04-22       Impact factor: 6.475

Review 8.  Molecular dynamics simulations in photosynthesis.

Authors:  Nicoletta Liguori; Roberta Croce; Siewert J Marrink; Sebastian Thallmair
Journal:  Photosynth Res       Date:  2020-04-15       Impact factor: 3.573

9.  Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

Authors:  Ido Y Ben-Shalom; Zhixiong Lin; Brian K Radak; Charles Lin; Woody Sherman; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2020-11-18       Impact factor: 6.006

10.  Impact of electronic polarizability on protein-functional group interactions.

Authors:  Himanshu Goel; Wenbo Yu; Vincent D Ustach; Asaminew H Aytenfisu; Delin Sun; Alexander D MacKerell
Journal:  Phys Chem Chem Phys       Date:  2020-04-06       Impact factor: 3.676

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