Abstract
Proteins use their functional regions to exploit various activities, including binding to other proteins, nucleic acids, or drugs. Functional sites of the proteins have a tendency to be more conserved than the rest of the protein surface. Therefore, detection of the conserved residues using phylogenetic analysis is a general approach to predict functionally critical residues. In this chapter, we describe some of the available methods to predict functional sites and demonstrate a complete pipeline with tool alternatives at several steps. We explain the standard procedure and all intermediate stages including homology detection with BLAST search, multiple sequence alignment (MSA) and the construction of a phylogenetic tree for a given query sequence. Additionally, we demonstrate the prediction results of these methods on a case study. Finally, we discuss the possible challenges and bottlenecks throughout the pipeline. Our step-by-step description about the functional site prediction could be a helpful resource for the researchers interested in finding protein functional sites, to be used in drug discovery research.
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Acknowledgements
H.A. acknowledges TUBITAK 2211 Doctoral Fellowship Program. N.T. thanks to the TUBITAK Career Development Program (Project no: 117E192). T.D. acknowledges TUBITAK BIDEB 2218 Program.
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Atas, H., Tuncbag, N., Doğan, T. (2018). Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. In: Gore, M., Jagtap, U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7756-7_4
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