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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

Matthew P Jacobson¹, Chakrapani Kalyanaraman¹, Suwen Zhao¹

¹Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA.

Trends in Biochemical Sciences

|July 7, 2014

Abstract:

The rapid growth of the number of protein sequences that can be inferred from sequenced genomes presents challenges for function assignment, because only a small fraction (currently <1%) has been experimentally characterized. Bioinformatics tools are commonly used to predict functions of uncharacterized proteins. Recently, there has been significant progress in using protein structures as an additional source of information to infer aspects of enzyme function, which is the focus of this review. Successful application of these approaches has led to the identification of novel metabolites, enzyme activities, and biochemical pathways. We discuss opportunities to elucidate systematically protein domains of unknown function, orphan enzyme activities, dead-end metabolites, and pathways in secondary metabolism.

Keywords:

docking enzyme function prediction homology modeling metabolic pathways protein structures

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