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Kumar, M., Agarwal, T., Khokhar, S., Kumar, M., Kaur, P., Roy, T.S. and Dada, R. (2011) Mutation screening and genotype phenotype correlation of a-crystallin, g-crystallin and GJA8 gene in congenital cataract. Molecular Vision, 17, 693-707.

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• TITLE: Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

  AUTHORS: Sigit Jaya Herlambang, Rosari Saleh

  KEYWORDS: Protein; Modeling; Mutation; Build Model Protocols

  JOURNAL NAME: Journal of Biophysical Chemistry, Vol.3 No.2, May 29, 2012

  ABSTRACT: Protein structure modeling using a homologous template is one of many routines that accompany the molecular dynamics simulation for biological material. There are currently two protocols of protein modeling available in Accelrys Discovery Studio 2.1, Build Mutants and Build Homology Modeling protocols. Both are template-based modeling, but with a different process. In this study, two different templates, 3CKZ and 274Y, have been used to see how much the differences will be made by those two protocols if the templates has significant percentage of identity. Evaluation of structure models has been performed using DOPE score, 3D-profile, and PROCHECK. The results indicated that Build Mutants Protocols produces more stable structures but has a low reliability values and low quality of stereochemistry when using a template that has a lower percentage of identity. The results also yield more stable, reliable, and higher percentage of residues in most favoured and additionally allowed region for the usage of Build Homology Modeling Protocol on both templates. These observations suggest that Build Homology Modeling protocol is recommended for protein modeling.