Novel computational biology methods and their applications to drug discovery

Abstract

Computational biology methods are now firmly entrenched in the drug discovery process. These methods focus on modeling and simulations of biological systems to complement and direct conventional experimental approaches. Two important branches of computational biology include protein homology modeling and the computational biophysics method of molecular dynamics. Protein modeling methods attempt to accurately predict three-dimensional (3D) structures of uncrystallized proteins for subsequent structure-based drug design applications. Molecular dynamics methods aim to elucidate the molecular motions of the static representations of crystallized protein structures. In this review we highlight recent novel methodologies in the field of homology modeling and molecular dynamics. Selected drug discovery applications using these methods conclude the review.

Keywords

computational biology / drug discovery / homology modeling / molecular dynamics / structure-based drug design

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Acknowledgments

This work was supported in part by the US Department of Defense Concept Awards (BC085871), US National Institute of Health P41 grant (5P41GM079588-03), and Grant # IRG-08-061-01 from the American Cancer Society to SZ. SSP was supported by UTHealth Innovation for Cancer Prevention Research Pre-doctoral Fellowship, The University of Texas School of Public Health – Cancer Prevention and Research Institute of Texas grant # RP101503.

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