Similar protocols

Pipeline publication

[…] od described in . Both enzyme and substrate controls were maintained throughout the assay procedure., The tertiary structure of EXNI protein was generated with the aid of MODELLER (version 9.13) program [, ]. The most similar X-ray crystallographic structures were identified in RSCB PDB protein databank [, ] using the Blast Protein tool [] against the deduced amino acid sequence of EXNI as the target. Multiple sequence alignment method was used for homology modeling and the generated model was based on the templates of PDB IDs: 2JIC, 4S2H, and 4HKW for EXNI in the RSCB PDB protein databank. The constructed model was validated using structure validation tools of VERIFY3D [], PROCHECK [], and ERRAT [] to analyze the compatibility of the model with its amino acid sequence, to verify the geometrical and stereochemical constraints of the model and to determine the overall quality factor respectively. The COACH server (https://zhanglab.ccmb.med.umich.edu/COACH) [, ] was used to identify the binding domain of the above generated EXNI model., The 3D structure of the oligoxylose ligand was constructed and geometrically optimized before docking, with 6-31g∗∗ basis set using Gaussian 09 (linux version) software []. Protein and above optimized ligand were prepared using UCSF chimera [], and the ligand docked into the active site of the model structure of EXNI using DOCK6 software [, ] using flexible docking method. The binding strength of the protein and the ligand was ranked using the grid score energies []., Molecular dynamics simulation was performed in two phases. In the first phase, the docked protein-ligand complex obtained from above docking process with lowest binding energy was selected as the initial configuration for the molecular dynamics (MD) simulations using the GROMACS v4.6.5 []. The GROMOS54a7 united atom force field was assigned for the model protein. The force field parameters of the ligand were obtained from PRODRG server []. The protein […]

Pipeline specifications

Software tools ERRAT, COACH, UCSF Chimera