Research Interests

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

Selected Publications

• Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol Cell. 30:137-144 (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 (E-pub ahead of print.) (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 sodels? 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).

• Schnieders, M.J., Baker, N.A., Ren, P., and Ponder, J.W. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J. Chem Phys 126:124114-12135 (2007).

• Cheng, Y., Suen, J.K., Zhang, D., Bond, S.D., Zhang, Y., Song, Y., Baker, N.A., Bajaj, C.L., Holst, M.J. and McCammon, J.A. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal 92:3397-3406(2007).