Protein 3D structure determination using homology modeling and structure analysis

S. Brindha, Sangzuala Sailo, Liansangmawii Chhakchhuak, Pranjal Kalita, G. Gurusubramanian, N. Senthil Kumar

Science Vision 11 (3), 125-133 | Published on 30 September 2011 |

Abstract

The protein sequence of aspartate aminotransferase of pig was retrieved from the Swiss-Prot database. The appropriate template for homology modeling was determined using Blastp. 3D structures were determined by homology modeling softwares such as Swiss Model and EsyPred3D which passed quality test by ProQ software and set for further analysis. The pockets determined by CASTp server for the predicted structures showed a significant difference in the pocket area and volume, which were due to structural deviation between the residues 30-40 found in the 3d-ss software. Both the structures were analyzed using ProFunc tool which showed different functions as they had different structures and active sites. Thus the structure plays a vital role in determining its function.

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