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Investigators and Program Directors

Nilesh Banavali

Nilesh Banavali

Research Scientist, Wadsworth Center,
Computational & Structural Biology

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 MacKerell Jr. A. D. (2009) Characterizing structural transitions using localized free energy landscape analysis. PLoS One 4:e5525.
  • Yang, S., Banavali, N.K. and Roux, B. (2009) Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc. Natl. Acad. Sci. U.S.A. 106:3776-3781.
  • Banavali, N.K. and Roux, B. (2009) Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins 74:378-389.
  • 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