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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[1] 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

* Corresponding Author