Publications Listed in NSF Biographical Sketch (PDF file is Linked, where available)

(A) Closely related to the Project

  1. N. Sreerama and R.W. Woody. Computation and Analysis of Protein Circular Dichroism Spectra. Meth. Enzymol. (in press) 2004. PDF File
  2. N. Sreerama and R.W. Woody. Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem.282, 252-260, 2000.  PDF File
  3. R.W. Woody and N. Sreerama. Comment on ‘Improving protein circular dichroism calculations in the far-ultraviolet through reparameterizing the amide chromophore’ [J. Chem. Phys. 109, 782 (1998)]. J. Chem. Phys. 111, 2844-2845, 1999. PDF File
  4.  N. Sreerama, S. Yu. Venyaminov, R. W. Woody, Estimation of the number of α-helical and β-strand segments in proteins using circular dichroism spectroscopy. Protein Sci. 8, 370-380, 1999. PDF File
  5. N. Sreerama and R.W. Woody. Poly(Pro)II type structure in globular proteins - Identification and CD analysis.  Biochemistry, 33, 10022-10025, 1994. PDF File

(B) Other Significant publications

  1. N. Sreerama and R.W. Woody, On the analysis of membrane protein circular dichroism spectra. Protein Sci. (in Press) 2004.  PDF File
  2. C. Kiefl, N. Sreerama, R. Haddad, L. Sun,  W. Jentzen, Y. Lu, Y. Qiu, J.A. Shelnutt, and R.W. Woody, Heme Distortions in Sperm-Whale Carbonmonoxy Myoglobin:  Correlations between Rotational Strengths and Heme Distortions in MD-Generated Structures. J. Am. Chem. Soc., 124, 3385-3394, 2002.  PDF File
  3. N. Sreerama, S.Y.Venyaminov and R.W. Woody, Analysis of Protein CD Spectra with A Reference Protein Set Based on Tertiary Structure Class. Anal. Biochem., 299, 271-274, 2001.  PDF File
  4.  N. Sreerama, M.C. Manning, ME. Powers, D.M. Goldenberg and R.W. Woody. Tyrosine, phenylalanine and disulfide contributions to the protein circular dichroism spectra: CD spectra of wild-type and mutant BPTI. Biochemistry, 38, 10814-10822, 1999.  PDF File
  5. N. Sreerama and R. W. Woody, Molecular dynamics simulations of polypeptide conformations in water: A comparison of alpha, beta and poly(Pro)II conformations, Proteins: Struct. Funct. Genet. 36, 400- 406, 1999. PDF File


All Publications (in Reverse Chronological Order) -- Linked to the PDF file where available


  1. N. Sreerama and R.W. Woody. (2004) Computation and Analysis of Protein Circular Dichroism Spectra. Meth. Enzymol. (in press). PDF File
  2. N. Sreerama and R.W. Woody. (2004) On the analysis of membrane protein circular dichroism spectra. Protein Sci. (in Press). PDF File
  3. N. Sreerama and R.W. Woody. (2003) Structural Composition of bI and bII Proteins. Protein Sci. 12, 384-388. PDF_File
  4. C. Kiefl, N. Sreerama, R. Haddad, L. Sun,  W. Jentzen, Y. Lu, Y. Qiu, J.A. Shelnutt, and R.W. Woody, (2002) Heme Distortions in Sperm-Whale Carbonmonoxy Myoglobin: Correlations between Rotational Strengths and Heme Distortions in MD-Generated Structures. J. Am. Chem. Soc. 124, 3385-3394. PDF_File
  5. R.W. Woody, C. Kiefl, N. Sreerama, Y. Lu, Y. Qiu, and J.A. Shelnutt. (2002) MD Simulations of carbonmonoxy myoglobin and calculations of heme CD. in Insulin and Related Proteins - From Structure to Function and Pharmacology (M Federwisch and M.L. Dieken, and P. de Meyts, Eds.), Kluwer Academic Publishers, Dordrecht, The Netherlands pp 233-248. (Invited Article) 
  6. T-C. Mou, N. Sreerama, T.C. Terwilliger, R.W. Woody, and D.M. Gray, (2002) Independent Tyrosyl Contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41F and Y41H mutants on protein-protein interactions. Protein Sci. 11, 601-613. PDF_File
  7. N. Sreerama, S.Y.Venyaminov and R.W. Woody, (2001) Analysis of Protein CD Spectra with A Reference Protein Set Based on Tertiary Structure Class. Anal. Biochem. 299, 271-274. PDF_File
  8. Y. Griko, N. Sreerama, P. Osumi-Davis, R.W. Woody and A-Y.W. Woody. (2001) Thermal and urea-induced unfolding in T7 RNA polymerase: Calorimetry, Circular Dichroism and Fluorescence study. Prot. Sci. 10, 845-853. PDF_File
  9. A. Koslowski, N. Sreerama and R.W. Woody. (2000) Theoretical Approach to Electronic Optical Activity. in Circular Dichroism: Principles and Applications, 2nd  ed. (Eds. N.Berova, K.Nakanishi, & R.W.Woody), John Wiley & Sons, Inc., New York. pp 55-96. (Book Chapter)
  10. N. Sreerama and R.W. Woody. (2000) Circular Dichroism of Peptides and Proteins.  in Circular Dichroism: Principles and Applications, 2nd  ed. (Eds. N.Berova, K.Nakanishi, & R.W.Woody), John Wiley & Sons, Inc., New York. pp 601-620. (Book Chapter)
  11. N. Sreerama, S.Y.Venyaminov and R.W. Woody. (2000) Estimation of protein secondary structure from CD spectra: Inclusion of denatured proteins with native protein in the analysis.  Anal. Biochem. 287, 243-251. PDF_File
  12. N. Sreerama and R.W. Woody. (2000) Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem. 282, 252-260. PDF_File
  13. N. Sreerama, S.Y.Venyaminov and R.W. Woody. (1999) Estimation of the number of alpha-helical and beta-sheet segments in proteins using circular dichroism spectroscopy.  Protein Science, 8, 370. PDF_File
  14. R.W. Woody and N. Sreerama. (1999) Comment on ‘Improving protein circular dichroism calculations in the far-ultraviolet through reparameterizing the amide chromophore’ [J. Chem. Phys. 109, 782 (1998)]. J. Chem. Phys. 111,  2844. PDF_File
  15. N. Sreerama, M.C. Manning, ME. Powers, D.M. Goldenberg and R.W. Woody. (1999) Tyrosine, phenylalanine and disulfide contributions to the protein circular dichroism spectra: CD spectra of wild-type and mutant BPTI. Biochemistry 38, 10814-10822. PDF File
  16. N. Sreerama and R.W. Woody. (1999) Molecular dynamics simulations of polypeptide conformations in water: A comparison alpha, beta and poly(Pro)II structures. Proteins: Struc. Func. Genet. 36, 400. PDF_File
  17. T.M. Thompson, B.L. Mark, C.L. Gray, T.C. Terwilliger, N. Sreerama, R.W. Woody and D.M. Gray. (1998) Circular dichroism and electron microscopy of a core Y61F mutant of the f1 gene 5 single-strand DNA binding protein, and theoretical analysis of CD spectra of four Tyr-Phe substitutions. Biochemistry, 37, 7463. PDF_File
  18. A.I. Meyers, T. Nguyen, D. Stoianova, N. Sreerama, R.W. Woody, A. Koslowski and J. Fleischhauer. (1997) Synthesis and chiroptical properties of a novel C2-Symmetric binaphthyl phosphortriamide (“chiral HMPA”). Chirality, 9, 431. PDF_File
  19. P.A. Osumi-Davis, N. Sreerama, D.B. Volkin, C.R. Middaugh, R.W. Woody and A-Y. M. Woody (1994) T7 RNA Polymerase and its active site mutants:  Kinetic, spectroscopic and calorimetric characterization.  J. Mol. Biol. 237, 5. PDF_File
  20. N. Sreerama and R.W. Woody (1994) Protein secondary structure from circular dichroism spectroscopy - Combining variable selection principle and cluster analysis with neural network, ridge regression and self-consistent methods. J. Mol.Biol., 242, 497. PDF_File
  21. N. Sreerama and R.W. Woody (1994) Poly(Pro)II type structure in globular proteins - Identification and CD analysis. Biochemistry, 33, 10022. PDF_File
  22. N. Sreerama, R.W. Woody and P.R. Callis (1994) Theoretical Study of the crystal field effects on the transition dipole moments in methylated adenines. J.Phys. Chem., 98, 10397. PDF_File
  23. G. Blauer, N. Sreerama and R.W. Woody (1993) Optical activity of hemoproteins in the Soret region. circular dichroism of the heme undecapeptide of cytochrome C in aqueous solution. Biochemistry, 32, 6674. PDF_File
  24. N. Sreerama and R.W. Woody (1993) A self consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochemistry, 209, 32. PDF_File
  25. R. Sankararamakrishnan, N. Sreerama and S. Vishveshwara. (1991) Characterization of proline containing right-handed  a-helix by molecular dynamics studies. Biophysical Chemistry, 40, 97. PDF_File
  26. N. Sreerama, M.C. Manning and R.W. Woody (1991) The circular dichroism of biopolymers: Aromatic side-chain CD in proteins.  Proc. 4th Int. Conf. CD, Bochum, p186. (Symp. Proceedings)
  27. N. Sreerama and S. Vishveshwara (1989) An ab initio study of the proton affinity of conjugated Schiff-base and related nitrogen compounds - An analysis of triggering site of bacteriorhodopsin.  J. Mol. Struc., 194, 61. PDF_File
  28. N. Sreerama and S. Vishveshwara (1989) An ab initio study of the proton affinity in (A1-H..A2)+ and (A-H..B)+ H-bonded systems.  J. Mol. Struc.,  212, 53. PDF_File
  29. N. Sreerama and S. Vishveshwara (1987) Molecular mechanism of facilitated transport by carrier ionophores: A study of energetics. J. Biosci., 12, 175. PDF_File
  30. N. Sreerama and S. Vishveshwara (1985) Studies involving electrostatic potential of valinomycin.  J. Biosci., 8, 315.  (Symp. Proceedings)
  31. N. Sreerama and S. Vishveshwara (1985) An ab initio study of (C-H...X)+ hydrogen bonds including biological systems.   J. Mol. Struc., 133, 139. PDF_File