Force field development and simulations of intrinsically disordered proteins
Jing Huang1, Alexander D MacKerell2
1Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn St., Baltimore, MD 21201, USA; Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 5635 Fishers Lane, Rockville, MD 20852, USA.
Abstract:
Intrinsically disordered proteins (IDPs) play important roles in many physiological processes such as signal transduction and transcriptional regulation. Computer simulations that are based on empirical force fields have been increasingly used to understand the biophysics of disordered proteins. In this review, we focus on recent improvement of protein force fields, including polarizable force fields, concerning their accuracy in modeling intrinsically disordered proteins. Some recent benchmarks and applications of these force fields are also overviewed.
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