Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

2018-03-01
Tunçbağ, Nurcan
Doğan, Tunca
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Proteins usetheir 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.
Drug discovery , Evolutionary conservation , Functional site , Multiple sequence alignment , Phylogenetic analysis , Predictive approaches
https://link.springer.com/book/10.1007/978-1-4939-7756-7
https://hdl.handle.net/11511/71392
Graduate School of Informatics, Book / Book chapter

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Citation Formats
N. Tunçbağ and T. Doğan, Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. 2018, p. 69.
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