MFCC-Based Fragmentation Methods for Biomolecules

Jinfeng Liu, Tong Zhu, Xiao He, John Z.H. 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

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Keywords

  • CPCM model
  • Energy calculation
  • MFCC-based fragmentation methods
  • Mechanical embedded-quantum mechanical approach
  • 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. Z. H. (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