Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of protein-targets.

Miryala, Sravan Kumar and Basu, Soumya and Naha, Aniket and Debroy, Reetika and Ramaiah, Sudha and Anbarasu, Anand and Natarajan, Saravanan (2022) Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of protein-targets. Data in brief, 42. p. 108146. ISSN 2352-3409

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Abstract

Docking scores and simulation parameters to study the potency of natural compounds against protein targets in (M) were retrieved through molecular docking and structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding M target proteins. M protein targets were actively involved in translation mechanism, nucleic acid metabolism and membrane integrity. Standard structural screening and stereochemical optimizations were adopted to generate the 3D protein structures and their corresponding ligands prior to molecular docking. Force-field integration and energy minimization were further employed to obtain the proteins in their ideal geometry. Surflex-dock algorithm using Hammerhead scoring functions were used to finally produce the docking scores between each protein and the corresponding ligand(s). The best-docked complexes selected for simulation studies were subjected to topology adjustments, charge neutralizations, solvation and equilibrations (temperature, volume and pressure). The protein-ligand complexes and molecular dynamics parameter files have been provided. The trajectories of the simulated parameters such as density, pressure and temperature were generated with integrated tools of the simulation suite. The datasets can be useful to computational and molecular medicine researchers to find therapeutic leads relevant to the chemical behaviours of a specific class of compounds against biological systems. Structural parameters and energy functions provided a set of standard values that can be utilised to design simulation experiments regarding similar macromolecular interactions.

Affiliation:	ICMR-National Institute for Research in Tuberculosis
Item Type:	Article
Uncontrolled Keywords:	Datasets, simulated protein-ligand complexes, SYBYL docking, bioactive, Mycobacterium tuberculosis, protein-targets
Subjects:	Tuberculosis > Laboratory Research > Biochemical
Divisions:	Basic Science Research > Biochemistry
Depositing User:	Dr. Rathinasabapati R
Date Deposited:	29 Mar 2023 06:47
Last Modified:	29 Mar 2023 07:01
URI:	http://eprints.nirt.res.in/id/eprint/1889

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