General transition-state force field for cytochrome p450 Hydroxylation
Rydberg, Patrik LU ; Olsen, Lars ; Norrby, Per-Ola and Ryde, Ulf LU
(2007)
In Journal of Chemical Theory and Computation
3(5).
p.1765-1773
- Abstract
- We have developed force-field parameters for the hydrogen-abstraction transition state of aliphatic hydroxylation by cytochrome P450 using the Q2MM approach. The parametrization is based on quantum chemical (B3LYP) transition-state structures and Hessian matrices for 24 diverse substrate models (14 in the training set and 10 in the test set). The force field is intended to be applicable to any druglike molecule by the use of the general Amber force field (GAFF) for the substrates. The parameters reproduce the geometries within 0.1 angstrom and 1.2 degrees for bond lengths and angles, respectively, with no significant differences between the training and test sets. The Hessian matrix is also well reproduced with a correlation coefficient of... (More)
- We have developed force-field parameters for the hydrogen-abstraction transition state of aliphatic hydroxylation by cytochrome P450 using the Q2MM approach. The parametrization is based on quantum chemical (B3LYP) transition-state structures and Hessian matrices for 24 diverse substrate models (14 in the training set and 10 in the test set). The force field is intended to be applicable to any druglike molecule by the use of the general Amber force field (GAFF) for the substrates. The parameters reproduce the geometries within 0.1 angstrom and 1.2 degrees for bond lengths and angles, respectively, with no significant differences between the training and test sets. The Hessian matrix is also well reproduced with a correlation coefficient of 0.99. The parametrization is performed by the ideal iterative approach of Norrby and Liljefors, which we have implemented for the Amber software. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/657319
- author
- Rydberg, Patrik
LU
; Olsen, Lars
; Norrby, Per-Ola
and Ryde, Ulf
LU
- organization
- publishing date
- 2007
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Theory and Computation
- volume
- 3
- issue
- 5
- pages
- 1765 - 1773
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000249454500012
- scopus:35948961951
- ISSN
- 1549-9618
- DOI
- 10.1021/ct700110f
- language
- English
- LU publication?
- yes
- additional info
- 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)
- id
- daf44db2-e503-4cb0-b4b6-779b388b394e (old id 657319)
- date added to LUP
- 2016-04-01 11:45:45
- date last changed
- 2023-03-09 18:33:03
@article{daf44db2-e503-4cb0-b4b6-779b388b394e,
abstract = {{We have developed force-field parameters for the hydrogen-abstraction transition state of aliphatic hydroxylation by cytochrome P450 using the Q2MM approach. The parametrization is based on quantum chemical (B3LYP) transition-state structures and Hessian matrices for 24 diverse substrate models (14 in the training set and 10 in the test set). The force field is intended to be applicable to any druglike molecule by the use of the general Amber force field (GAFF) for the substrates. The parameters reproduce the geometries within 0.1 angstrom and 1.2 degrees for bond lengths and angles, respectively, with no significant differences between the training and test sets. The Hessian matrix is also well reproduced with a correlation coefficient of 0.99. The parametrization is performed by the ideal iterative approach of Norrby and Liljefors, which we have implemented for the Amber software.}},
author = {{Rydberg, Patrik and Olsen, Lars and Norrby, Per-Ola and Ryde, Ulf}},
issn = {{1549-9618}},
language = {{eng}},
number = {{5}},
pages = {{1765--1773}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Chemical Theory and Computation}},
title = {{General transition-state force field for cytochrome p450 Hydroxylation}},
url = {{https://lup.lub.lu.se/search/files/136746349/101_p450forcefield.pdf}},
doi = {{10.1021/ct700110f}},
volume = {{3}},
year = {{2007}},
}