Computational protocol: In-silico and In-vitro based studies of Streptomyces peucetius CYP107N3 for oleic acid epoxidation

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Protocol publication

[…] The computer-based analyses and comparison of protein sequences were performed using the programs BLAST, FASTA, CLUSTALW and GENEDOC. The homology modeling of CYP107N3 and docking were performed using Accelrys Discovery Studio V3.1 (Accelrys Software Inc., San Diego, CA, USA). The homologue search was done from the ExPASy web site (http://swissmodel.expasy.org). The structures of three highly homologous proteins, 2D0E (CYP158A2, 2.15 Å, length 407 aa) , 2ZBX (CYP105A1, 1.5 Å, length 412 aa) and 3E5L (CYP105P1, 2.40 Å, length 403 aa) were selected as templates for modeling. The final 3D model was generated by MODELER, an original program that performed automatic protein homology modeling and loop modeling for CYP107N3. The refined model was validated with ProSa2003 , and Ramachandran Plot . RSMD (Root Mean Square Deviation) analysis of the predicted model from its templates was calculated using SUPERPOSE . Substrate for docking was drawn using a sketch toolbar application and converted to stereo-chemically correct configuration and optimized by Dreiding-like force-field in DS V3.1. The protein-ligand interaction study was performed using LigandFit/LigandScore , an automated tool for protein-small molecule docking/scoring. […]

Pipeline specifications

Software tools Clustal W, SuperPose, PHENIX
Databases ExPASy
Application Protein structure analysis
Organisms Escherichia coli
Diseases Multiple Sclerosis
Chemicals Fatty Acids, Oleic Acid