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      LiGRO: a graphical user interface for protein-ligand molecular dynamics.

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          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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          Author and article information

          Journal
          J Mol Model
          Journal of molecular modeling
          Springer Nature America, Inc
          0948-5023
          0948-5023
          Oct 04 2017
          : 23
          : 11
          Affiliations
          [1 ] 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. luciano.kagami@ufrgs.br.
          [2 ] 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.
          [3 ] Universal Protein Resource (UniProt), EMBL-EBI, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
          [4 ] Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, Brazil.
          [5 ] Health Sciences Postgraduate Program of Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite Street, n° 245, 2nd Floor, room 200C, Porto Alegre City, Rio Grande do Sul State, Brazil.
          [6 ] Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP), Cândido Portinari Street, n° 200, Campinas, SP, 13083-871, Brazil.
          [7 ] Institute of Chemistry, University of Campinas (UNICAMP), Josué de Castro Street, Campinas, SP, 13083-970, Brazil.
          [8 ] 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. veraeifler@ufrgs.br.
          Article
          10.1007/s00894-017-3475-9
          10.1007/s00894-017-3475-9
          28980073
          07269d4e-5df7-4966-8264-5f14c1b12490
          History

          Protein-ligand,Molecular dynamics and ACPYPE,Graphical user interface,Gromacs

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