title: An Improved Protein Surface Extraction Method Using Rotating Cylinder Probe.
abstract: 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.
authors.affiliation: Division of Applied Science, Indian Institute of Information Technology, Jhalwa Campus, Allahabad, UP, 211012, India.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Singh
authors.affiliation: Division of Applied Science, Indian Institute of Information Technology, Jhalwa Campus, Allahabad, UP, 211012, India. tlahiri@iiita.ac.in.
authors.forename: Tapobrata
authors.initials: T
authors.lastname: Lahiri
mesh_terms: D001665:Binding Sites; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000302:isolation & purification*
chemical_list: D011506:Proteins
keywords: Binding sites qualifying surfaces; Comparison of extracted surfaces; Protein surface; Rotating cylinder probe; Surface extraction method