©2021-2032 All Rights Reserved. Online Journal of Bioinformatics. You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to firstname.lastname@example.org publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. Linking: To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
Online Journal of Bioinformatics©
Volume 22 (2): 103-110, 2021.
Protein surface extracting software for active site residues
Kalpana Singh1, Manoj Kumar Pal1, Tapobrata Lahiri Apurba Kumar Samal2
1Department of Applied Science, Indian Institute of Information Technology, Allahabad, India
2Indegene Life systems, Bengaluru, India
Singh K, Pal MK, Lahiri T, Samal ASK., Protein surface extracting algorithms for active site residues, Onl J Bioinform., 22 (2): 103-110, 2021. Software should be able to access functional atoms on surface protein. We used algorithms to access surfaces of 90 PDB-proteins with known functional sites from Catalytic Site Atlas including functional atoms discovering 2457 residue proteins in active sites. The molecular surface algorithm extracted 52%, Surface Racer 75% chothia’s Van der waals radii 79% and Lahiri 58%. Active site information should be in the cavity but we found less active site residues there that on outer surface. Our results suggest conventional algorithms were unable to effectively retrieve outer surface active or functional sites.
Key words: Protein surface, protein active site, software comparison