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SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites

Sankar, S and Chandra, N (2022) SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites. In: PLoS Computational Biology, 18 (2).

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Official URL: https://doi.org/10.1371/journal.pcbi.1009901


Studying similarities in protein molecules has become a fundamental activity in much of biology and biomedical research, for which methods such as multiple sequence alignments are widely used. Most methods available for such comparisons cater to studying proteins which have clearly recognizable evolutionary relationships but not to proteins that recognize the same or similar ligands but do not share similarities in their sequence or structural folds. In many cases, proteins in the latter class share structural similarities only in their binding sites. While several algorithms are available for comparing binding sites, there are none for deriving structural motifs of the binding sites, independent of the whole proteins. We report the development of SiteMotif, a new algorithm that compares binding sites from multiple proteins and derives sequence-order independent structural site motifs. We have tested the algorithm at multiple levels of complexity and demonstrate its performance in different scenarios. We have benchmarked against 3 current methods available for binding site comparison and demonstrate superior performance of our algorithm. We show that SiteMotif identifies new structural motifs of spatially conserved residues in proteins, even when there is no sequence or fold-level similarity. We expect SiteMotif to be useful for deriving key mechanistic insights into the mode of ligand interaction, predict the ligand type that a protein can bind and improve the sensitivity of functional annotation.

Item Type: Journal Article
Publication: PLoS Computational Biology
Publisher: Public Library of Science
Additional Information: The copyright for this article belongs to the Authors.
Keywords: algorithm; article; binding site; intermethod comparison; ligand binding; binding site; chemistry, ligand; protein; protein binding, Algorithms; Binding Sites; Ligands; Protein Binding; Proteins
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Date Deposited: 24 Jun 2022 07:36
Last Modified: 24 Jun 2022 07:36
URI: https://eprints.iisc.ac.in/id/eprint/73883

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