MFCC-Based Fragmentation Methods for Biomolecules

Jinfeng Liu, Tong Zhu, Xiao He, John Zhang

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

This chapter describes the molecular fractionation with conjugate caps (MFCC)-based fragmentation methods and their applications to biological systems. To account for the environmental polarization effect for each fragment calculation, electrostatic embedding was introduced into the GMFCC/molecular mechanics (MM) method which became the latest electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method for more accurate calculation of the protein energy. The EE-GMFCC method is computationally efficient and linear-scaling with a low prefactor, and has been successfully applied to protein geometry optimization, molecular dynamics simulation, protein-ligand binding affinity calculation, and protein vibrational spectrum calculation at QM levels. The chapter combines the more accurate EE-GMFCC method with the CPCM model, denoted as EE-GMFCC-CPCM, for accurate calculation of protein solvation energy. To reduce the computational cost, the mechanical embedded (ME)-quantum mechanical (QM)/MM approach is used to describe the protein dynamics in explicit solvent while the water molecules are described by mechanical mechanics.

Original languageEnglish (US)
Title of host publicationFragmentation
Subtitle of host publicationToward Accurate Calculations on Complex Molecular Systems
Publisherwiley
Pages323-348
Number of pages26
ISBN (Electronic)9781119129271
ISBN (Print)9781119129240
DOIs
StatePublished - Jun 21 2017

Fingerprint

Biomolecules
Fractionation
Proteins
Molecular mechanics
Solvation
Vibrational spectra
Biological systems
Molecular dynamics
Electrostatics
Mechanics
Polarization
Ligands
Molecules
Geometry
Water
Computer simulation
Costs

Keywords

  • CPCM model
  • Energy calculation
  • Mechanical embedded-quantum mechanical approach
  • MFCC-based fragmentation methods
  • Molecular mechanics
  • Protein geometry optimization
  • Protein solvation energy
  • Protein-ligand binding energy
  • Vibrational spectrum

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Liu, J., Zhu, T., He, X., & Zhang, J. (2017). MFCC-Based Fragmentation Methods for Biomolecules. In Fragmentation: Toward Accurate Calculations on Complex Molecular Systems (pp. 323-348). wiley. https://doi.org/10.1002/9781119129271.ch11

MFCC-Based Fragmentation Methods for Biomolecules. / Liu, Jinfeng; Zhu, Tong; He, Xiao; Zhang, John.

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. wiley, 2017. p. 323-348.

Research output: Chapter in Book/Report/Conference proceedingChapter

Liu, J, Zhu, T, He, X & Zhang, J 2017, MFCC-Based Fragmentation Methods for Biomolecules. in Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. wiley, pp. 323-348. https://doi.org/10.1002/9781119129271.ch11
Liu J, Zhu T, He X, Zhang J. MFCC-Based Fragmentation Methods for Biomolecules. In Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. wiley. 2017. p. 323-348 https://doi.org/10.1002/9781119129271.ch11
Liu, Jinfeng ; Zhu, Tong ; He, Xiao ; Zhang, John. / MFCC-Based Fragmentation Methods for Biomolecules. Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. wiley, 2017. pp. 323-348
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