PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

Sung Bo Hwang; Chang Joon Lee; Sehan Lee; Songling Ma; Young Mook Kang; Kwang Hwi Cho; Su Yeon Kim; Oh Young Kwon; Chang No Yoon; Young Kee Kang; Jeong Hyeok Yoon; Ky Youb Nam; Seong Gon Kim; Youngyong In; Han Ha Chai; William E. Acree; J. Andrew Grant; Ken D. Gibson; Mu Shik Jhon; Harold A. Scheraga; Kyoung Tai No

doi:10.1021/acs.jpcb.9b10339

PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

Sung Bo Hwang, Chang Joon Lee, Sehan Lee, Songling Ma, Young Mook Kang, Kwang Hwi Cho, Su Yeon Kim, Oh Young Kwon, Chang No Yoon, Young Kee Kang, Jeong Hyeok Yoon, Ky Youb Nam, Seong Gon Kim, Youngyong In, Han Ha Chai, William E. Acree, J. Andrew Grant, Ken D. Gibson, Mu Shik Jhon, Harold A. ScheragaKyoung Tai No

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

Original language	English
Pages (from-to)	974-989
Number of pages	16
Journal	Journal of Physical Chemistry B
Volume	124
Issue number	6
DOIs	https://doi.org/10.1021/acs.jpcb.9b10339
Publication status	Published - 2020 Feb 13

Bibliographical note

Funding Information:
This study was supported by BMDRC. K.T.N. thanks H.A.S. for waiting 25 years for this study. We thank Late Dr. Mu Shik Jhon for many helpful discussions. H.A.S. thanks the National Institutes of Health (GM-14312) for the support.

Publisher Copyright:
Copyright © 2020 American Chemical Society.

All Science Journal Classification (ASJC) codes

Physical and Theoretical Chemistry
Surfaces, Coatings and Films
Materials Chemistry

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10.1021/acs.jpcb.9b10339

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Hwang, S. B., Lee, C. J., Lee, S., Ma, S., Kang, Y. M., Cho, K. H., Kim, S. Y., Kwon, O. Y., Yoon, C. N., Kang, Y. K., Yoon, J. H., Nam, K. Y., Kim, S. G., In, Y., Chai, H. H., Acree, W. E., Grant, J. A., Gibson, K. D., Jhon, M. S., ... No, K. T. (2020). PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking. Journal of Physical Chemistry B, 124(6), 974-989. https://doi.org/10.1021/acs.jpcb.9b10339

@article{23daab42b06740e8b329357018609dd3,

title = "PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking",

abstract = "The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term {"}physics-based{"} is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.",

author = "Hwang, {Sung Bo} and Lee, {Chang Joon} and Sehan Lee and Songling Ma and Kang, {Young Mook} and Cho, {Kwang Hwi} and Kim, {Su Yeon} and Kwon, {Oh Young} and Yoon, {Chang No} and Kang, {Young Kee} and Yoon, {Jeong Hyeok} and Nam, {Ky Youb} and Kim, {Seong Gon} and Youngyong In and Chai, {Han Ha} and Acree, {William E.} and Grant, {J. Andrew} and Gibson, {Ken D.} and Jhon, {Mu Shik} and Scheraga, {Harold A.} and No, {Kyoung Tai}",

note = "Funding Information: This study was supported by BMDRC. K.T.N. thanks H.A.S. for waiting 25 years for this study. We thank Late Dr. Mu Shik Jhon for many helpful discussions. H.A.S. thanks the National Institutes of Health (GM-14312) for the support. Publisher Copyright: Copyright {\textcopyright} 2020 American Chemical Society.",

year = "2020",

month = feb,

day = "13",

doi = "10.1021/acs.jpcb.9b10339",

language = "English",

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Hwang, SB, Lee, CJ, Lee, S, Ma, S, Kang, YM, Cho, KH, Kim, SY, Kwon, OY, Yoon, CN, Kang, YK, Yoon, JH, Nam, KY, Kim, SG, In, Y, Chai, HH, Acree, WE, Grant, JA, Gibson, KD, Jhon, MS, Scheraga, HA & No, KT 2020, 'PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking', Journal of Physical Chemistry B, vol. 124, no. 6, pp. 974-989. https://doi.org/10.1021/acs.jpcb.9b10339

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T2 - Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

AU - Hwang, Sung Bo

AU - Lee, Chang Joon

AU - Lee, Sehan

AU - Ma, Songling

AU - Kang, Young Mook

AU - Cho, Kwang Hwi

AU - Kim, Su Yeon

AU - Kwon, Oh Young

AU - Yoon, Chang No

AU - Kang, Young Kee

AU - Yoon, Jeong Hyeok

AU - Nam, Ky Youb

AU - Kim, Seong Gon

AU - In, Youngyong

AU - Chai, Han Ha

AU - Acree, William E.

AU - Grant, J. Andrew

AU - Gibson, Ken D.

AU - Jhon, Mu Shik

AU - Scheraga, Harold A.

AU - No, Kyoung Tai

N1 - Funding Information: This study was supported by BMDRC. K.T.N. thanks H.A.S. for waiting 25 years for this study. We thank Late Dr. Mu Shik Jhon for many helpful discussions. H.A.S. thanks the National Institutes of Health (GM-14312) for the support. Publisher Copyright: Copyright © 2020 American Chemical Society.

PY - 2020/2/13

Y1 - 2020/2/13

N2 - The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

AB - The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

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U2 - 10.1021/acs.jpcb.9b10339

DO - 10.1021/acs.jpcb.9b10339

M3 - Article

C2 - 31939671

AN - SCOPUS:85079348305

SN - 1520-6106

VL - 124

SP - 974

EP - 989

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 6

ER -

PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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