LiGRO: a graphical user interface for protein–ligand molecular dynamics
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/ ..
| Medienart: |
Artikel |
|---|
| Erscheinungsjahr: |
2017 |
|---|---|
| Erschienen: |
2017 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:23 |
|---|---|
| Enthalten in: |
Journal of molecular modeling - 23(2017), 11, Seite 1-6 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Kagami, Luciano Porto [VerfasserIn] |
|---|
| Links: |
|---|
| doi: |
10.1007/s00894-017-3475-9 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
OLC1999786696 |
|---|
| LEADER | 01000caa a2200265 4500 | ||
|---|---|---|---|
| 001 | OLC1999786696 | ||
| 003 | DE-627 | ||
| 005 | 20230507090926.0 | ||
| 007 | tu | ||
| 008 | 171228s2017 xx ||||| 00| ||eng c | ||
| 024 | 7 | |a 10.1007/s00894-017-3475-9 |2 doi | |
| 028 | 5 | 2 | |a PQ20171228 |
| 035 | |a (DE-627)OLC1999786696 | ||
| 035 | |a (DE-599)GBVOLC1999786696 | ||
| 035 | |a (PRQ)p1002-ed01d64d233ecec980163f7f2302c5a715cacdafa96ec35b81d236b056def4450 | ||
| 035 | |a (KEY)0523238420170000023001100001ligroagraphicaluserinterfaceforproteinligandmolecu | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 082 | 0 | 4 | |a 30 |q DNB |
| 082 | 0 | 4 | |a 570 |q AVZ |
| 084 | |a 35.06 |2 bkl | ||
| 100 | 1 | |a Kagami, Luciano Porto |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a LiGRO: a graphical user interface for protein–ligand molecular dynamics |
| 264 | 1 | |c 2017 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ohne Hilfsmittel zu benutzen |b n |2 rdamedia | ||
| 338 | |a Band |b nc |2 rdacarrier | ||
| 520 | |a 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/ . | ||
| 540 | |a Nutzungsrecht: © Springer-Verlag GmbH Germany, part of Springer Nature 2017 | ||
| 650 | 4 | |a Theoretical and Computational Chemistry | |
| 650 | 4 | |a Computer Applications in Chemistry | |
| 650 | 4 | |a Chemistry | |
| 650 | 4 | |a Computer Appl. in Life Sciences | |
| 650 | 4 | |a Gromacs | |
| 650 | 4 | |a Protein-ligand | |
| 650 | 4 | |a Molecular dynamics and ACPYPE | |
| 650 | 4 | |a Graphical user interface | |
| 650 | 4 | |a Molecular Medicine | |
| 650 | 4 | |a Characterization and Evaluation of Materials | |
| 650 | 4 | |a Libraries | |
| 650 | 4 | |a Energy conservation | |
| 650 | 4 | |a Topology | |
| 650 | 4 | |a Molecular dynamics | |
| 650 | 4 | |a Proteins | |
| 650 | 4 | |a Docking | |
| 650 | 4 | |a Downloading | |
| 650 | 4 | |a Design modifications | |
| 650 | 4 | |a Ligands | |
| 650 | 4 | |a Parametrization | |
| 650 | 4 | |a Mathematical analysis | |
| 700 | 1 | |a das Neves, Gustavo Machado |4 oth | |
| 700 | 1 | |a da Silva, Alan Wilter Sousa |4 oth | |
| 700 | 1 | |a Caceres, Rafael Andrade |4 oth | |
| 700 | 1 | |a Kawano, Daniel Fábio |4 oth | |
| 700 | 1 | |a Eifler-Lima, Vera Lucia |4 oth | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of molecular modeling |d Berlin : Springer, 2003 |g 23(2017), 11, Seite 1-6 |w (DE-627)362900760 |w (DE-600)2108012-4 |w (DE-576)105215732 |x 1610-2940 |7 nnns |
| 773 | 1 | 8 | |g volume:23 |g year:2017 |g number:11 |g pages:1-6 |
| 856 | 4 | 1 | |u http://dx.doi.org/10.1007/s00894-017-3475-9 |3 Volltext |
| 856 | 4 | 2 | |u https://search.proquest.com/docview/1947102483 |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a SYSFLAG_A | ||
| 912 | |a GBV_OLC | ||
| 912 | |a SSG-OLC-PHA | ||
| 912 | |a SSG-OLC-DE-84 | ||
| 912 | |a GBV_ILN_70 | ||
| 912 | |a GBV_ILN_267 | ||
| 912 | |a GBV_ILN_2018 | ||
| 912 | |a GBV_ILN_2219 | ||
| 936 | b | k | |a 35.06 |q AVZ |
| 951 | |a AR | ||
| 952 | |d 23 |j 2017 |e 11 |h 1-6 | ||