Similar protocols

Pipeline publication

[…] b'tional studies were performed on Intel Xeon Quad core (2.33 GHz processor) server installed with LINUX OS (openSUSE Version 12.0). Multiple sequence alignment was carried out by ClustalW of the closest homologue identified by NCBI p-Blast to find out the identity, similarity and gap region between the target and template []. Homology modeling was accomplished by ORCHESTRAR [] implemented in BioPolymer module of SYBYL7.3 []. An online server, I-TASSER [], was used for modeling a region absent in template structure. The finally selected model of hs\xce\xb2ADR1was minimized by AMBER (Version10.0) []. Stereochemical properties of modeled protein structure were validated by PROCHECK [], Verify3D [] and ERRAT []. Molecular docking experiments were conducted by Surflex-Dock implemented in SYBYL (Version 7.3) [], FRED (Version 2.2.5) [] and GOLD (Version 2.5) []. UCSF CHIMERA [\xe2\x80\x93] and MOE [] were used for visualization purpose. The flowchart of work plan is illustrated in ()., The sequence of hs\xce\xb2ADR1 (AC No: P08588) was retrieved from UniProt KB []. This target sequence comprises of 477 amino acid residues was submitted to NCBI-Protein BLAST [] to search the closest homologue. Top-ranked template sequences as determined by BLAST were subjected for multiple sequence alignment on the basis of optimized E-value of the specified target sequence (). However, Meleagris gallopavo \xce\xb21-AR (Mg\xce\xb2ADR1, PDB ID: 2Y00) retrieved as the closest homologue, was manually edited for optimal alignment along with the target sequence. Best alignment was selected based on alig' […]

Pipeline specifications

Software tools ERRAT, Surflex-Dock, UCSF Chimera