Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase英文文献资料.docVIP

Vol.3, No.2, 183-190 (2012) Journal of Biophysical Chemistry /10.4236/jbpc.2012.32020 Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase Sigit Jaya Herlambang , Rosari Saleh * Departemen Fisika, Fakultas MIPA, Universitas Indonesia, Depok, Indonesia; Corresponding Author: sigit.jaya.herlambang@ * Received 1 March 2012; revised 22 March 2012; accepted 11 April 2012 ABSTRACT doubt that the x-ray structure crystallography takes much time and involves difficult methods which requires sig- nificant amount of expertise and resources to generate only one protein structure. To deal with this problem, many alternative methods have been developed. Among them, there are two protocols in Accelrys Discovery Studio 2.1 which adopted MODELLER program [3], Build Ho- mology Modeling and Build Mutants protocols, to gen- erate structure models based on their templates. It has been generally known that the medium identity percentage of the sequences resulted only slight differ- ences in their 3D structure [4]. Although the results of homology models still need an assessment, the perform- ance of Build Homology Modeling protocol has been well understood and documented [5,6]. These protein structure prediction protocol could build backbone, side- chains, loop (if needed), and any necessary cofactors and ligand. In contrast to the Build Homology Modeling protocol, Build Mutants protocol uses the template without chang- ing backbone, side-chains, loop and any necessary cofa- ctors and ligand. This protocol mutates one or more residues of wild-type protein and optimizes the local structure in the specified range while the outside radius is made fix. Therefore, the local energy minimization that occurs will greatly affect if the mutated residues are quite a lot. Both Build Homology Modeling and Build Mutants protocols were used to generate H5N1 avian i