Pratul K. Agarwal Associate Staff Scientist, Oak Ridge National Laboratory Computational Biology Institute, Computer Science and Mathematics Division http://www.vigyaancd.org/pratul/ PhD: Computational Biochemistry and Biophysics, Pennsylvania State University (2002) MT: Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi (1997) BT: Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi (1995) Oak Ridge National Lab Bldg. 5600 MS 6016 865-574-7184 agarwalpk@ornl.gov

Keywords:
Multi-scale modeling to investigate protein folding, structure, dynamics and function. High performance computing strategies in biology. Linus software workbench for bio/chemical computing.

Research Area:

Description of Research:

Selected Publications (of 10):

• Agarwal, P.K.(2005) (). 'Role of Protein Dynamics in Reaction Rate Enhancement by Enzymes'. J. Am. Chem. Soc(2005) 127, 15248-15256.


• Agarwal, P.K.; Geist, A.; Gorin, A.(2004) (). 'Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl-Prolyl cis/trans Isomerization Activity of Cyclophilin A'. Biochemistry (2004) 43, 10605-10618.


• Agarwal, P.K.(2004) (). 'Computational studies of the mechanism of cis/trans isomerization in HIV-1 catalyzed by cyclophilin A'. Proteins: Struct. Funct. Bioinformatics (2004) 56, 449-463.
  


• Watney, J.B.; Agarwal, P.K.; Hammes-Schiffer, S.(2003) (). 'Effect of mutation on enzyme motion in dihydrofolate reductase'. J. Am. Chem. Soc. (2003) 125, 3745-3750.
  


• Agarwal, P.K.; Billeter, S.R.; Hammes-Schiffer, S.(2002) (). 'Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis'. J. Phys. Chem B (2002) 106, 3283-3293.
  


• Agarwal, P.K.; Billeter, S.R.; Rajagopalan, P.T.R.; Benkovic, S.J.; Hammes-Schiffer, S. (2002) (). 'Network of Coupled Promoting Motions in Enzyme Catalysts'. Proc. Natl. Acad.Sci. USA (2002) 99, 2794-2799.
  


• Billeter, S.R.; Webb, S.P.; Agarwal, P.K.; Iordanov, T.; Hammes-Schiffer, S. (2001) (). 'Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and the Role of Enzyme Motion'. J. Am. Chem.Soc. (2001) 123, 11262-11272.
  


• Billeter, S.R.; Webb, S.P.; Iordanov, T.; Agarwal, P.K. (2001) (). 'Hybrid Approach for Including Electronic and Nuclear Quantum Effects in Molecular Dynamics Simulations of Hydrogen Transfer Reactions in Enzymes'. J. Chem. Phys. (2001) 114, 6925-6936.
  


• Webb, S.P.; Agarwal, P.K.; Hammes-Schiffer, S.(2000) (). 'Combining Electronic Structure Methods with Calculation of Hydrogen Vibrational Wavefunctions: Application to Hydride Transfer Catalyzed by Liver Alcohol Dehydrogenase'. J. Phys. Chem B. (2000) 104, 8884-8894.

Invited Reviews and Book Chapters:

• Agarwal, P.K.(2005) (). 'Enzymes: An integrated view of structure, protein dynamics and function'. Microbial Cell Factories.