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Pipeline publication

[…] A) was selected by performing BLAST search against protein databank (PDB) with > 80% sequence identity cut off for homology modeling. Alignment between target KN sequence (KN-MurF Ligase) and the template Escherichia coli (EC) sequence (EC-MurF Ligase, PDB ID: 1GG4_A) was performed with Multalin tool and visualized using ES pript [, ]., Tertiary structure prediction was performed using I-Tasser Server for homology modeling []. The plausible models of KN-MurF obtained from I-Tasser server were verified by Structural Analysis and Verification Server (SAVES) to evaluate its stereo-chemical quality [, ]., The structures of 14 phyto-ligands and 1 antibiotic, Ciprofloxacin, were sketched with Accelrys Draw (v4.0). Each structure was launched in ligprep (Schrödinger) and energy minimized using the OPLS force field and geometrically optimized followed by Lipinski's values/ADME-Tox prediction by using Qikprop (Schrödinger)., Docking analysis of KN-MurF1 was carried out using Autodock (v4.2) with the aim of exposing the active site amino acid residues involving protein-ligand interactions so as to obtain information about the bioactive conformation of these KNMurF inhibitors. From the ADT package hydrogen atoms were added, Nonpolar hydrogens and lone pairs were merged and each atom within the macromolecule was assigned a Gasteiger partial charge. A grid box of 80×80×80, with a spacing of 0.447 Å was positioned using autogrid and blind docking was performed. The Lamarckian genetic algorithm (LGA) of up to 20 runs was employed with the settings of population size of 150 individuals, maximum […]

Pipeline specifications

Software tools BIOVIA Draw, LigPrep, QikProp