Research Interests

Computational biology: multiscale modeling of biological process, biomolecular solvation, protein structure and dynamics

Selected Publications

• Dong, F., Wagoner, J.A. and Baker, N.A. Assessing the performance of implicit solvation models at a nucleic acid surface. Phys. Chem. Chem. Phys. 10:4889-4902, (2008).

• Bradley, M.J., Chivers, P.T. and Baker, N.A. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol. 378:1155-1173 (2008).

• Lee, S.J., Song, Y. and Baker, N.A. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: Potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J. 94:3565-3576 (2008).

• Dong, F., Olsen, B. and Baker, N.A. Computational methods for biomolecular electrostatics. Methods Cell Biol. 84:843-870 (2008).

• Cerutti, D.S., Baker, N.A. and McCammon, J.A. Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? J Chem Phys. 127:155101-155113 (2007).

• Dolinsky, T.J., Czodrowski, P., Li, H., Nielson, J.E., Jensen, J.H., Klebe, G. and Baker, N.A. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35:W522-W525 (2007).