Discovery studio or Molegro virtual docker: out of both which one is the best tool for docking? Asked 29th May, 2020; Deepak Verma. Molegro Virtual Docker is an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker is a protein-ligand docking simulation program that allows us to carry out docking simulations in a fully integrated computational package. MVD has been successfully applied to hundreds of different proteins, with docking performance similar to other docking programs such as A. Data Modelling and Analysis. The ‘Molegro Data Modeller’ product bundled with MVD makes it possible to create regression and classification models, extract statistical measures, and visualize data. Predict numerical properties of docked compounds from MVD docking runs. User-created models can be applied directly in the Pose Organizer.
Molegro Virtual Docker Free Download
Richa Anand
Department of Biochemical Engineering, Banaras Hindu university, UP, India.
ABSTRACT
Mycobacterium tuberculosis a causative agent of tuberculosis is gram-positive and slow growing bacterium. Decaprenyl-phosphoryl-β-D-ribose oxidase is an important enzyme involved in the cell wall synthesis of Mycobacterium tuberculosis. It is involved in the epimerization of decaprenyl-phosphoryl-D-ribose into decaprenyl-phosphoryl-D-arabinose, a precursor for arabinan synthesis. Its 3-D structure has not yet been reported either by X-ray crystallography or NMR. Therefore, model of decaprenyl-phosphoryl-β-D-ribose oxidase was determined by homology modeling, using multi-template approach based on crystal structure of 2EXR.pdb and 2Q4W.pdb with score=48.9 bits and identities=42/148 (29%). The computed model was subjected to refinement on the basis of consensus generated from 2D structure. The energy minimization and molecular dynamics simulation was performed by DESMOND using OPLS-AA force field and finally evaluated using SAVES server to obtain reliable structure. The modeled protein was used for structure-based virtual screening against ZINC database through molecular docking using Molegro Virtual Docker (MVD) 4.2.0. Out of 19365 ZINC database molecules, top 10 docked complexes obtained after virtual screening were enumerated and validated based on Molegro Virtual Docker 4.2.0 Scoring function and ADME properties. On the basis of docking energies top 10 ligands were selected for validation using AutoDock/Vina scoring function to compare their results. Thus the complex scoring, docking energies and binding affinities revealed that these ligand molecules could be promising inhibitors for decaprenyl-phosphoryl-beta-D-ribose-2′-oxidase. The docking studies also reveal that Tyr (335), Thr (426) are prominently involved in hydrogen bond interactions with the ligands and thus they are important determinant residues in binding with ligands. Read more…
Richa Anand
Department of Biochemical Engineering, Banaras Hindu university, UP, India.
ABSTRACT
Molegro Virtual Docker Free Download
Mycobacterium tuberculosis a causative agent of tuberculosis is gram-positive and slow growing bacterium. Decaprenyl-phosphoryl-β-D-ribose oxidase is an important enzyme involved in the cell wall synthesis of Mycobacterium tuberculosis. It is involved in the epimerization of decaprenyl-phosphoryl-D-ribose into decaprenyl-phosphoryl-D-arabinose, a precursor for arabinan synthesis. Its 3-D structure has not yet been reported either by X-ray crystallography or NMR. Therefore, model of decaprenyl-phosphoryl-β-D-ribose oxidase was determined by homology modeling, using multi-template approach based on crystal structure of 2EXR.pdb and 2Q4W.pdb with score=48.9 bits and identities=42/148 (29%). The computed model was subjected to refinement on the basis of consensus generated from 2D structure. The energy minimization and molecular dynamics simulation was performed by DESMOND using OPLS-AA force field and finally evaluated using SAVES server to obtain reliable structure. The modeled protein was used for structure-based virtual screening against ZINC database through molecular docking using Molegro Virtual Docker (MVD) 4.2.0. Out of 19365 ZINC database molecules, top 10 docked complexes obtained after virtual screening were enumerated and validated based on Molegro Virtual Docker 4.2.0 Scoring function and ADME properties. On the basis of docking energies top 10 ligands were selected for validation using AutoDock/Vina scoring function to compare their results. Thus the complex scoring, docking energies and binding affinities revealed that these ligand molecules could be promising inhibitors for decaprenyl-phosphoryl-beta-D-ribose-2′-oxidase. The docking studies also reveal that Tyr (335), Thr (426) are prominently involved in hydrogen bond interactions with the ligands and thus they are important determinant residues in binding with ligands. Read more…