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Can I read Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana on EtoBox?
Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana by Akinori Hirashima; Hongwei Huang is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana about?
AY333178 (from Periplaneta americana, 628 AAs) was selected as a target octopamine receptor (OAR) class OAR2 for this study using Discovery Studio (DS Modeling1.1/1.2, Accelrys Inc.). Blast similarity search was performed and identified that AY333178 contains N-terminal domain of GPCR. Based upon Blast and Pfam results, Rhodopsin 1U19 (protein data bank) was considered as an ideal homologue and used as a template for homology modeling due to its higher X-ray resolution at 2.2 Å. Sequence alignment between AY333178 and 1U19 was done using Align123 followed by a manual modification. The final alignment was carefully evaluated and evidenced to be matching the conserved residue data for class A GPCR fairly well. The 3D model of AY333178 was generated with MODELER, and further refined using CHARMm. Superimposition of the model was done over the template 1U19. Two fairly consistent profiles were observed demonstrating AY333178 model was reasonable and could be employed for the further docking study. Agonist docking into OAR2 model was done using LigandFit. The superimposition of two top poses of representative agonists was performed with a soft surface generated. Those models are conside
Who reads Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Akinori Hirashima; Hongwei Huang
- Publisher
- Elsevier Science; Elsevier ; Elsevier Ltd.; Elsevier BV (ISSN 1476-9271)
- Published
- 2008
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)