LiGRO: a graphical user interface for protein-ligand molecular dynamics.
J Mol Model
; 23(11): 304, 2017 Oct 04.
Article
em En
| MEDLINE
| ID: mdl-28980073
ABSTRACT
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http//www.ufrgs.br/lasomfarmacia/ligro/ .
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
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Proteínas
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Descoberta de Drogas
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Simulação de Dinâmica Molecular
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Ligantes
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article