分子动力学
对接(动物)
码头
生物信息学
结核分枝杆菌
计算生物学
力场(虚构)
蛋白质-配体对接
分子力学
化学
计算化学
虚拟筛选
计算机科学
生物化学
生物
肺结核
医学
护理部
病理
人工智能
基因
作者
Sravan Kumar Miryala,Soumya Basu,Aniket Naha,Reetika Debroy,Sudha Ramaiah,Anand Anbarasu,Saravanan Natarajan
出处
期刊:Data in Brief
[Elsevier]
日期:2022-04-01
卷期号:42: 108146-108146
被引量:2
标识
DOI:10.1016/j.dib.2022.108146
摘要
Docking scores and simulation parameters to study the potency of natural compounds against protein targets in Mycobacterium tuberculosis (M tb ) were retrieved through molecular docking and in-silico structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding M tb target proteins. M tb 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.
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