Literature DB >> 26967542

Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

Wesley K Lay1, Mark S Miller1, Adrian H Elcock1.   

Abstract

GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.

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Year:  2016        PMID： 26967542      PMCID： PMC5082696          DOI： 10.1021/acs.jctc.5b01136

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  21 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Molecular dynamics simulations of solvated crystal models of cellulose I(alpha) and III(I).

Authors:  Toshifumi Yui; Sachio Hayashi
Journal:  Biomacromolecules       Date:  2007-02-08       Impact factor: 6.988

3.  Development of the CHARMM Force Field for Lipids.

Authors:  R W Pastor; A D Mackerell
Journal:  J Phys Chem Lett       Date:  2011       Impact factor: 6.475

4.  Theory and Simulation of Multicomponent Osmotic Systems.

Authors:  Sadish Karunaweera; Moon Bae Gee; Samantha Weerasinghe; Paul E Smith
Journal:  J Chem Theory Comput       Date:  2012-10-09       Impact factor: 6.006

5.  Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields.

Authors:  Jörg Sauter; Andrea Grafmüller
Journal:  J Chem Theory Comput       Date:  2015-03-23       Impact factor: 6.006

6.  CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Authors:  Elizabeth Hatcher; Olgun Guvench; Alexander D Mackerell
Journal:  J Phys Chem B       Date:  2009-09-17       Impact factor: 2.991

7.  Additive empirical force field for hexopyranose monosaccharides.

Authors:  Olgun Guvench; Shannon N Greene; Ganesh Kamath; John W Brady; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2008-11-30       Impact factor: 3.376

8.  Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields.

Authors:  Jejoong Yoo; Aleksei Aksimentiev
Journal:  J Chem Theory Comput       Date:  2015-12-16       Impact factor: 6.006

9.  GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

Authors:  Karl N Kirschner; Austin B Yongye; Sarah M Tschampel; Jorge González-Outeiriño; Charlisa R Daniels; B Lachele Foley; Robert J Woods
Journal:  J Comput Chem       Date:  2008-03       Impact factor: 3.376
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  13 in total

1.  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

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

Review 3.  Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.

Authors:  Robert J Woods
Journal:  Chem Rev       Date:  2018-08-09       Impact factor: 60.622

4.  Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

Authors:  Mark S Miller; Wesley K Lay; Shuxiang Li; William C Hacker; Jiadi An; Jianlan Ren; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-03-27       Impact factor: 6.006

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

Authors:  Marcelo D Polêto; Justin A Lemkul
Journal:  Commun Chem       Date:  2022-03-18

6.  Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.

Authors:  Wesley K Lay; Mark S Miller; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-04-28       Impact factor: 6.006

Review 7.  New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

Authors:  Jejoong Yoo; Aleksei Aksimentiev
Journal:  Phys Chem Chem Phys       Date:  2018-03-28       Impact factor: 3.676

8.  Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

Authors:  Jejoong Yoo; James Wilson; Aleksei Aksimentiev
Journal:  Biopolymers       Date:  2016-10       Impact factor: 2.505

9.  Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds.

Authors:  Katsufumi Tomobe; Eiji Yamamoto; Dušan Kojić; Yohei Sato; Masato Yasui; Kenji Yasuoka
Journal:  Sci Adv       Date:  2017-12-22       Impact factor: 14.136

10.  Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study.

Authors:  Lingshuang Song; Lin Yang; Jie Meng; Sichun Yang
Journal:  J Phys Chem Lett       Date:  2017-01-03       Impact factor: 6.475
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