An Improved Protein Surface Extraction Method Using Rotating Cylinder Probe
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For extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods. Also, a new surface extraction method is introduced based on the use of a rotating cylinder probe adapting from the work of Weisel et al. (Chem Cent J 1:7–23, 2007. doi: 10.1186/1752-153X-1-7). The result of the new method shows a significant improvement of performance in comparison to the existing methods.
KeywordsProtein surface Comparison of extracted surfaces Binding sites qualifying surfaces Rotating cylinder probe Surface extraction method
The authors gratefully acknowledge the grant-in-aid received from Indian Council of Medical Research (Project Sanction Letter No. 52/8/2005-BMS, dated February 4, 2010) to Tapobrata Lahiri to pursue this paper work.
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