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Investigators and Program Directors

Nilesh Banavali

Nilesh Banavali

Research Scientist, Wadsworth Center, Laboratory of Structural Pathology
Assistant Professor, School of Public Health, Biomedical Sciences

Ph.D., University of Maryland, Baltimore (2001)
Postdoctoral training, Weill Medical College of Cornell University, University of Chicago

E-mail: banavali@wadsworth.org

<<Research Interests

Select Publications

  • Banavali, N.K. and Roux, B. (2007) The Anatomy of a Structural Pathway for Activation of the Catalytic Domain of Src Kinase Hck. Proteins 67:1096-1112 (Featured on Cover).
  • Macias, A.T., Banavali, N.K. and MacKerell Jr., A.D. (2007) DNA bending induced by carbocyclic sugar analogs constrained to the north conformation. Biopolymers 85:438-449.
  • Banavali, N.K. and MacKerell Jr., A.D. (2006) Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. J. Phys. Chem. B 110:10997-11004.
  • Banavali, N.K. and Roux, B. (2005) The N-terminal end of the catalytic domain of Src kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure 13:1715-1723.
  • Banavali, N.K. and Roux, B. (2005) Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J. Am. Chem. Soc. 127:6866-6876.
  • Horton J.R., Ratner, G., Banavali, N.K., Huang, N., Choi, Y., Maier, M., Marquez, V.E., MacKerell Jr., A.D., and Cheng X. (2004) Caught in the act: visualization of an intermediate iin the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res. 32:3877-3886.
  • Huang, N., Banavali, N.K. and MacKerell Jr. A. D. (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. U.S.A. 100:68-73.
  • Banavali, N.K. and Roux, B. (2002) Atomic radii for continuum electrostatic calculations on nucleic acids. J. Phys. Chem. B 106:11026-11035.
  • Banavali, N.K., Im W., and Roux, B. (2002) Electrostatic free energy calculations using the generalized solvent boundary potential method. J. Chem. Phys. 117:7381-7388.
  • Banavali, N.K. and MacKerell Jr., A.D. (2002) Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol. 319:141-160.
  • Banavali, N.K. and MacKerell Jr., A.D. (2001) Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3-phosphoramidate moieties of nucleic acids. J. Am. Chem. Soc. 123:6747-6755.
  • Banavali, N.K. and MacKerell Jr., A.D. (2001) Reexamination of intrinsic, dynamic, and hydration properties of phosphoramidate DNA. Nucleic Acids Res. 29:3219-3230.
  • Wang, P., Brank, A.S., Banavali, N.K., Nicklaus, M.C., Marquez, V.E., Christman, J., and MacKerell Jr., A.D. (2000) Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI (cytosine C5)-methyltransferase J. Am. Chem. Soc. 122:12422-12434.
  • MacKerell Jr., A.D. and Banavali, N.K. (2000) All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution. J. Comp. Chem. 21:105-120.

Contact Information

Telephone: (518) 474-0569
Fax: (518) 402-4623
E-mail: banavali@wadsworth.org