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 journalArticle

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 languageEnglish
Pages (from-to)974-989
Number of pages16
JournalJournal of Physical Chemistry B
Volume124
Issue number6
DOIs
Publication statusPublished - 2020 Feb 13

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Fingerprint Dive into the research topics of 'PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking'. Together they form a unique fingerprint.

  • Cite this

    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