MzDOCK: A free ready-to-use GUI-based pipeline for molecular docking simulations.
J Comput Chem
; 45(23): 1980-1986, 2024 Sep 05.
Article
em En
| MEDLINE
| ID: mdl-38703357
ABSTRACT
Molecular docking is by far the most preferred approach in structure-based drug design for its effectiveness to predict the scoring and posing of a given bioactive small molecule into the binding site of its pharmacological target. Herein, we present MzDOCK, a new GUI-based pipeline for Windows operating system, designed with the intent of making molecular docking easier to use and higher reproducible even for inexperienced people. By harmonic integration of python and batch scripts, which employs various open source packages such as Smina (docking engine), OpenBabel (file conversion) and PLIP (analysis), MzDOCK includes many practical options such as binding site configuration based on co-crystallized ligands; generation of enantiomers from SMILES input; application of different force fields (MMFF94, MMFF94s, UFF, GAFF, Ghemical) for energy minimization; retention of selectable ions and cofactors; sidechain flexibility of selectable binding site residues; multiple input file format (SMILES, PDB, SDF, Mol2, Mol); generation of reports and of pictures for interactive visualization. Users can download for free MzDOCK at the following link https//github.com/Muzatheking12/MzDOCK.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Simulação de Acoplamento Molecular
Idioma:
En
Revista:
J Comput Chem
Assunto da revista:
QUIMICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Índia