Open Access
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
Leela S Dodda
1, 2, 3
,
Israel Cabeza De Vaca
1, 2, 3
,
J. Tirado-Rives
1, 2, 3
,
William Jorgensen
1, 2, 3
Publication type: Journal Article
Publication date: 2017-04-21
scimago Q1
wos Q1
SJR: 7.776
CiteScore: 31.7
Impact factor: 13.1
ISSN: 03051048, 13624962
PubMed ID:
28444340
Genetics
Abstract
The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.
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1.4k
Total citations:
1380
Citations from 2024:
639
(46.43%)
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GOST
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Dodda L. S. et al. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands // Nucleic Acids Research. 2017. Vol. 45. No. W1. p. W331-W336.
GOST all authors (up to 50)
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Dodda L. S., Cabeza De Vaca I., Tirado-Rives J., Jorgensen W. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands // Nucleic Acids Research. 2017. Vol. 45. No. W1. p. W331-W336.
Cite this
RIS
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TY - JOUR
DO - 10.1093/nar/gkx312
UR - https://doi.org/10.1093/nar/gkx312
TI - LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
T2 - Nucleic Acids Research
AU - Dodda, Leela S
AU - Cabeza De Vaca, Israel
AU - Tirado-Rives, J.
AU - Jorgensen, William
PY - 2017
DA - 2017/04/21
PB - Oxford University Press
SP - W331-W336
IS - W1
VL - 45
PMID - 28444340
SN - 0305-1048
SN - 1362-4962
ER -
Cite this
BibTex (up to 50 authors)
Copy
@article{2017_Dodda,
author = {Leela S Dodda and Israel Cabeza De Vaca and J. Tirado-Rives and William Jorgensen},
title = {LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands},
journal = {Nucleic Acids Research},
year = {2017},
volume = {45},
publisher = {Oxford University Press},
month = {apr},
url = {https://doi.org/10.1093/nar/gkx312},
number = {W1},
pages = {W331--W336},
doi = {10.1093/nar/gkx312}
}
Cite this
MLA
Copy
Dodda, Leela S., et al. “LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands.” Nucleic Acids Research, vol. 45, no. W1, Apr. 2017, pp. W331-W336. https://doi.org/10.1093/nar/gkx312.