Robert Best, Ph.D.



LABORATORY OF CHEMICAL PHYSICS
NIDDK, National Institutes of Health
Building 5 , Room 130
5 Memorial Dr.
Bethesda, MD 20814
Tel: 301-496-5414
Fax: 301-496-0825
Email: robert.best2@nih.gov

Robert Best

Research Website:


Education / Previous Training and Experience:

M.Sc. University of Cape Town (2000)
Ph.D. University of Cambridge (2003)
Royal Society University Research Fellow (2007-2012)


Research Statement:

My research is concerned with the dynamics of large biomolecules, in particular with protein dynamics, folding and misfolding. Novel simulation and theoretical methods are developed as needed to address specific problems. A strong emphasis is placed on making a connection with experiment, both in using experimental data to help improve simulation methodology or sampling, and simulations as a tool to assist the interpretation of experimental results.

Recent work has included the optimization of protein force fields using empirical data for peptides and macromolecules in solution, interpretation of single molecule fluorescence or pulling experiments using simulation and theory, coarse-grained master equations as a tool for interpreting peptide dynamics in simulations, diffusion models of protein folding, the binding mechanism of intrinsically disordered proteins, the influence of molecular chaperonins on folding and misfolding, the mechanism of substrate transport in hydrogenase enzymes and methods for identifying cryptic binding pockets in proteins.



Selected Publications:

Yaw Sing Tan, Pawel Sledz, Steffen Lang, Christopher J. Stubbs, David R. Spring, Chris Abell and Robert B. Best. Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of Polo-Like Kinase 1 Angew. Chem., 51: 10078-10081, 2012. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best, Jeetain Mittal, Michael Feig and Alexander D. MacKerell Jr. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of alpha-helix and beta-hairpin formation Biophys. J., 103: 1045-1051, 2012. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro Lopes, Jeetain Mittal, Michael Feig and Alexander D. MacKerell Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi,psi and side-chain chi1 and chi2 dihedral angles J. Chem. Theor. Comput., 8: 3257-3273, 2012. [Full Text/Abstract] Exit Disclaimer.

Apratim Bhattacharya, Robert B. Best and Jeetain Mittal. Smoothing of the GB1 Hairpin Folding Landscape by Interfacial Confinement. Biophys. J., 103: 596-600, 2012. [Full Text/Abstract] Exit Disclaimer.

Michael Knott and Robert B. Best. A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations. PLoS Comp. Biol., 8:e1002605, 2012. [Full Text/Abstract] Exit Disclaimer.

Julius Schulz, Lennart Schmidt, Robert B. Best, Joachim Dzubiella and Roland Netz. Peptide Chain Dynamics in Light and Heavy Water: Zooming in on Internal Friction. J. Am. Chem. Soc., 134: 6273-6279, 2012. [Full Text/Abstract] Exit Disclaimer.

Petra Kuhrova, Alfonso de Simone, Michal Otyepka and Robert B. Best. Force field dependence of chignolin folding and misfolding: comparison with experiment and redesign. Biophys. J., 102: 1897-1906, 2012. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best, David de Sancho and Jeetain Mittal. Residue-specific alpha-helix propensities from molecular simulation. Biophys. J., 102: 1462-1467, 2012. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best. Atomistic Molecular Simulations of Protein Folding. Curr. Opin. Struct. Biol., 22:52-61, 2012. [Full Text/Abstract] Exit Disclaimer.

Olga K. Dudko, Thomas G. W. Graham and Robert B. Best. Locating the folding barrier for single molecules under force. Phys. Rev. Lett., 107:208301, 2011. [Full Text/Abstract] Exit Disclaimer.

David de Sancho and Robert B. Best. Modulation of IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP. Mol. Biosystems, 8: 256-267, 2011. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best and Gerhard Hummer. Diffusion Models of Protein Folding. Phys. Chem. Chem. Phys, 13:16902-16911, 2011. [Full Text/Abstract] Exit Disclaimer.

Robert B. Best and Jeetain Mittal. Microscopic events in beta-hairpin folding from alternative unfolded ensembles. Proc. Natl. Acad. Sci. U. S. A., 108:11087-11092, 2011. [Full Text/Abstract] Exit Disclaimer.

Madeleine B. Borgia and Alessandro Borgia and Robert B. Best and Annette Steward and Daniel Nettels and Bengt Wunderlich and Benjamin Schuler and Jane Clarke. Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature, 474:662-665, 2011. [Full Text/Abstract] Exit Disclaimer.

David de Sancho and Robert B. Best. What is the time scale for alpha-helix nucleation? J. Am. Chem. Soc, 133:6809-6816, 2011. [Full Text/Abstract] Exit Disclaimer.




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Page last updated: February 08, 2013

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