Computational protocol: Antinociceptive Activity of Borreria verticillata: In vivo and In silico Studies

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Protocol publication

[…] The MD simulations of the complexes selected after molecular docking were performed using GROMACS 4.6.7 software (Berk et al., ) following Ramos et al. (). The ligand topologies were generated with Automated Topology Builder (ATB) and Repository version 2.1 (Malde et al., ). The protonation states of histidine residues were determined using the H++ online server—http://biophysics.cs.vt.edu/hppdetails.php. To enlarge the sample, 3 10-ns MD simulations were performed per complex using different atomic velocities assigned according to the Maxwell distribution. The data generated for the last 4 ns in each simulated system were used for analysis. During the production step, 123 frames were obtained at 100-ps intervals. The details of the interactions were calculated with LigPlot++ software (Laskowski et al., ). A minimum of 50% of contact (total of hydrophobic interactions and hydrogen bonds) in the analyzed frames was defined as a criterion of binding efficacy. […]

Pipeline specifications

Software tools GROMACS, H++
Application Protein physicochemical analysis
Organisms Rattus norvegicus, Mus musculus
Diseases Genetic Diseases, Inborn
Chemicals Formaldehyde, Indomethacin, Memantine, Sodium Chloride, N-Methylaspartate