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• W4310239552 abstract "The fragment molecular orbital (FMO) method is a fast quantum-mechanical method that divides systems into pieces of fragments and performs ab initio calculations. The system truncation enables further speed improvement. In this article, we systematically study the effects of system truncations on binding affinity calculations obtained with FMO in combination with either the polarizable continuum model (FMO/PCM) or in combination with the Møller-Plesset method (FMO-MP2). We have used five protein complexes with ligands of several charged states. The calculated binding energies of the size variants of the truncated system, including only a restricted number of atoms around the ligand, are compared to the energy obtained from a full system. The result shows that the systems could be truncated to a radius of 8 Å from neutral ligands within an error of 0.7 kcal/mol, and 12 Å from charged ligands within an error of 1.1 kcal/mol for calculating the binding energy in solution." @default.
• W4310239552 created "2022-11-30" @default.
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• W4310239552 date "2022-11-29" @default.
• W4310239552 modified "2023-09-30" @default.
• W4310239552 title "System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study" @default.
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• W4310239552 doi "https://doi.org/10.1002/jcc.27044" @default.
• W4310239552 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36444861" @default.
• W4310239552 hasPublicationYear "2022" @default.
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