Kagami Luciano Porto, das Neves Gustavo Machado, da Silva Alan Wilter Sousa, Caceres Rafael Andrade, Kawano Daniel Fábio, Eifler-Lima Vera Lucia
Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil.
Universal Protein Resource (UniProt), EMBL-EBI, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
J Mol Model. 2017 Oct 4;23(11):304. doi: 10.1007/s00894-017-3475-9.
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/ .
为了加快药物发现过程，在GROMACS中执行的分子动力学（MD）计算可以与对接模拟相结合，用于大型化合物库的筛选后分析。这需要在不同软件中生成配体的拓扑结构，具备一些Linux命令行的基本知识，以及对处理输出文件有一定的熟悉程度。这里介绍的基于Python的图形界面LiGRO旨在通过允许对GROMACS（MD和分析）、ACPYPE（配体拓扑结构构建器）和PLIP（蛋白质-配体相互作用监测器）进行图形化（非基于命令行）控制来克服这些蛋白质-配体参数化挑战，这些程序可以一起使用，以全面执行和分析复杂MD模拟的输出（包括能量最小化和NVT/NPT平衡）。通过允许以简单快速的方式计算线性相互作用能，LiGRO可用于药物发现流程，以选择具有更好蛋白质结合相互作用特征的化合物。LiGRO的设计允许研究人员自由下载和修改该软件，其源代码可根据GPLv3许可条款从http://www.ufrgs.br/lasomfarmacia/ligro/获取。
