A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.

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@article{4d55ab0822e7425bacfe4d31d3ed54c7,
title = "A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.",
abstract = "We present a combination of semiempirical quantum-mechanical (SQM) calculations in the conductor-like screening model with the MM/GBSA (molecular-mechanics with generalized Born and surface-area solvation) method for ligand-binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen-bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol-derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen-bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3-1.6 times larger than for MM/GBSA. {\circledC} 2012 Wiley Periodicals, Inc.",
author = "Paulius Mikulskis and Samuel Genheden and Karin Wichmann and Ulf Ryde",
note = "The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)",
year = "2012",
doi = "10.1002/jcc.22949",
language = "English",
volume = "33",
pages = "1179--1189",
journal = "Journal of Computational Chemistry",
issn = "1096-987X",
publisher = "John Wiley & Sons",
number = "12",

}