Literature DB >> 35382231

Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.

Marcelo D Polêto1, Justin A Lemkul1,2.   

Abstract

The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergence of polarizable force fields and the role of electronic polarization and areas in which additive force fields fall short. The use of automated fitting methods and the inclusion of additional experimental solution data during parametrization is discussed as a means to highlight possible routes to improve the accuracy of force fields even further.

Entities:  

Year:  2022        PMID: 35382231      PMCID: PMC8979544          DOI: 10.1038/s42004-022-00653-z

Source DB:  PubMed          Journal:  Commun Chem        ISSN: 2399-3669


  90 in total

1.  Protein Circular Dichroism Data Bank (PCDDB): data bank and website design.

Authors:  Lee Whitmore; Robert W Janes; B A Wallace
Journal:  Chirality       Date:  2006-06       Impact factor: 2.437

2.  Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.

Authors:  Mark S Miller; Wesley K Lay; Adrian H Elcock
Journal:  J Phys Chem B       Date:  2016-04-21       Impact factor: 2.991

3.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

Authors:  Nathan Schmid; Andreas P Eichenberger; Alexandra Choutko; Sereina Riniker; Moritz Winger; Alan E Mark; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2011-04-30       Impact factor: 1.733

4.  Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins.

Authors:  Sheng Yang; Hao Liu; Yangpeng Zhang; Hui Lu; Haifeng Chen
Journal:  J Chem Inf Model       Date:  2019-10-22       Impact factor: 4.956

5.  Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization.

Authors:  Esther Heid; Markus Fleck; Payal Chatterjee; Christian Schröder; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2019-03-12       Impact factor: 6.006

6.  Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties.

Authors:  Giulio Tesei; Thea K Schulze; Ramon Crehuet; Kresten Lindorff-Larsen
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-02       Impact factor: 11.205

7.  Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.

Authors:  Gerhard König; Bernard R Brooks
Journal:  Biochim Biophys Acta       Date:  2014-09-16

8.  Systematic validation of protein force fields against experimental data.

Authors:  Kresten Lindorff-Larsen; Paul Maragakis; Stefano Piana; Michael P Eastwood; Ron O Dror; David E Shaw
Journal:  PLoS One       Date:  2012-02-22       Impact factor: 3.240

9.  ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost.

Authors:  J S Smith; O Isayev; A E Roitberg
Journal:  Chem Sci       Date:  2017-02-08       Impact factor: 9.825

10.  Developing a molecular dynamics force field for both folded and disordered protein states.

Authors:  Paul Robustelli; Stefano Piana; David E Shaw
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-07       Impact factor: 11.205

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