high-throughput conformation generator tool. Moreover, to study the protein–ligand
complexes for the simulated systems, in-house developed tool was used. Docked
pose of one of ligand is shown in Fig. 17. Preliminary analyses have been completed
for the systems. The hydrogen bond and water density analyses have been performed
using the in-house developed big data analytics tool, HBAT. MSM analyses are also
being carried out for the same, and the results are being compared with the wild-type
counterpart. Further, MD simulations were carried out for the best molecule per site
in order to check the binding of the molecule with Ras (data unpublished). Classical
simulations have been carried out using GROMACS software on Bioinformatics
Resource and Applications Facility (BRAF). The standard protocol has been followed for minimization, heating, equilibration, and production run.
Fig. 17 KRas protein with ligand docked at SITE2
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complexes for the simulated systems, in-house developed tool was used. Docked
pose of one of ligand is shown in Fig. 17. Preliminary analyses have been completed
for the systems. The hydrogen bond and water density analyses have been performed
using the in-house developed big data analytics tool, HBAT. MSM analyses are also
being carried out for the same, and the results are being compared with the wild-type
counterpart. Further, MD simulations were carried out for the best molecule per site
in order to check the binding of the molecule with Ras (data unpublished). Classical
simulations have been carried out using GROMACS software on Bioinformatics
Resource and Applications Facility (BRAF). The standard protocol has been followed for minimization, heating, equilibration, and production run.
Fig. 17 KRas protein with ligand docked at SITE2
Turbo Analytics: Applications of Big Data and HPC in Drug …
369