Výsledky vyhledávání - "Wesley K. Lay"

Reparameterization of Solute—Solute Interactions for Amino Acid–Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

Autor: Wesley K. Lay, Mark S. Miller, Adrian H. Elcock

Publikováno v: Journal of Chemical Theory and Computation. 13:1874-1882

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid–sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa4fe51f2c044eac87eb8ca62476c467
https://doi.org/10.1021/acs.jctc.7b00194

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Optimizing computer simulation models for carbohydrates and proteins at the atomistic and coarse-grained level

Autor: Wesley K. Lay

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::747495416c74b75a0b154a9bc8f6713b
https://doi.org/10.17077/etd.ske0-s6gc

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

Autor: Wesley K. Lay, Mark S. Miller, Adrian H. Elcock

Publikováno v: Journal of chemical theory and computation. 13(6)

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental os

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3dd95f9b83970c050cf562d013e28c6b
https://pubmed.ncbi.nlm.nih.gov/28437100

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

Autor: Wesley K. Lay, Adrian H. Elcock, Jianlan Ren, Shuxiang Li, Jiadi An, Mark S. Miller, William C. Hacker

Publikováno v: Journal of chemical theory and computation. 13(4)

There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparameterize simulation force fields. Here we have investigated the ability of five very commonly used force field and water mo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19406f9d2643b385baf1b0912e974947
https://pubmed.ncbi.nlm.nih.gov/28296391

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

Autor: Adrian H. Elcock, Mark S. Miller, Wesley K. Lay

Publikováno v: The journal of physical chemistry. B. 120(33)

Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b18ecada91fd17207d2650b18d12f967
https://pubmed.ncbi.nlm.nih.gov/27052117

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

Autor: Mark S. Miller, Wesley K. Lay, Adrian H. Elcock

Publikováno v: Journal of chemical theory and computation. 12(4)

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 glucos

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ada748b71e799d0971ff50c45377cca
https://pubmed.ncbi.nlm.nih.gov/26967542

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