A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.
Forskningsoutput: Tidskriftsbidrag › Artikel i vetenskaplig tidskrift
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. © 2012 Wiley Periodicals, Inc.
Detaljer
Författare | |
---|---|
Enheter & grupper | |
Forskningsområden | Ämnesklassifikation (UKÄ) – OBLIGATORISK
|
Originalspråk | engelska |
---|---|
Sidor (från-till) | 1179-1189 |
Tidskrift | Journal of Computational Chemistry |
Volym | 33 |
Utgåva nummer | 12 |
Status | Published - 2012 |
Publikationskategori | Forskning |
Peer review utförd | Ja |
Nedladdningar
Ingen tillgänglig data
Relaterad forskningsoutput
Samuel Genheden, 2012, Department of Chemistry, Lund University. 330 s.
Forskningsoutput: Avhandling › Doktorsavhandling (sammanläggning)