Selected older publications (all so-twentieth century!)

Some of my earlier papers that are still of greatest interest are listed here.


Reviews

  • D. A. Case. Electronic structure calculations using the Xα method. Annu. Rev. Phys. Chem. 33, 151-171 (1982).

  • D.A. Case. Dynamical simulation of rate constants in protein-ligand interactions. Prog. in Biophys. and Mol. Biol. 52, 39-70 (1989).

  • C.L. Brooks, III and D.A. Case. Simulations of peptide conformational dynamics and thermodynamics. Chem. Rev. 93, 2487-2502 (1993).

  • L. Noodleman and D.A. Case. Density functional theory of spin polarization and spin coupling in iron-sulfur clusters. Adv. Inorg. Chem. 38, 423-470 (1992).

  • R. Brüschweiler and D.A. Case. Characterization of biomolecular structure and dynamics by NMR cross relaxation. Prog. NMR Spectr. 26, 27-58 (1994).

  • D.A. Case. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4, 285-290 (1994).

  • D.A. Case, H.J. Dyson and P.E. Wright. Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins. Meth. in Enzymol. 239, 392-416 (1994).

  • L. Noodleman, C.Y. Peng, D.A. Case and J.M. Mouesca. Orbital interactions, electron delocalization, and spin interactions in iron-sulfur clusters. Coord. Chem. Rev. 144, 199-244 (1995).

  • D.A. Case. Chemical shifts of amino acids, peptides and proteins. In Encylopedia of Nuclear Magnetic Resonance, D.M. Grant and R.K. Harris, eds. (London, John Wiley, 1996), pp. 751-755.

  • P. Beroza and D.A. Case. Calculations of proton binding thermodynamics in proteins. Meth. Enzymol. 295, 170-189 (1998).

  • D. Sitkoff and D.A. Case. Theories of chemical shift anisotropies in proteins and nucleic acids. Prog. NMR Spectr. 32, 165-190 (1998).

  • D.A. Case. NMR spectral simulation and structure refinement. In Encyclopedia of Computational Chemsistry (Chichester: John Wiley, 1998), pp. 1866-1876.

  • P. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case and T.E. Cheatham, III. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accts. Chem. Res. 33, 889-897 (2000).

  • D.A. Case. Interpretation of chemical shifts and coupling constants in macromolecules. Curr. Opin. Struct. Biol. 10, 197-203 (2000).


    Other older publications

  • D. A. Case and D. R. Herschbach. Statistical theory of angular momentum polarization in chemical reactions. Mol. Phys. 30, 1537-1564 (1975). [This paper was reprinted in 2002 as a part of a collection of 18 of the most significant papers published in the first 100 volumes of the journal: Mol. Phys. 100, 109-125 (2002). See also the commentary by D.C. Cleary: Mol. Phys. 100, 107 (2002).]

  • D. A. Case, G. M. McClelland and D. R. Herschbach. Angular momentum polarization in molecular collisions: classical and quantum theory for measurements using resonance fluorescence. Mol. Phys. 35, 541-573 (1978).

  • D. A. Case and M. Karplus. Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132, 343-368 (1979). [This paper has been cited more than 420 times, according to the ISI Web of Science.]

  • A. Aizman and D. A. Case. Electronic structure calculations on active site models for 4-Fe, 4-S iron-sulfur proteins. J. Am. Chem. Soc. 104, 3269-3279 (1982).

  • S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona and P. Weiner. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784 (1984). [This paper is the 10th most highly cited paper in the 125 year history of this journal, and has been cited more than 3,600 times. See J. Am. Chem. Soc. 125, 1-8 (2003).]

  • D. T. Nguyen and D. A. Case. On finding stationary states of large molecule potential energy surfaces. J. Phys. Chem. 89, 4020-4026 (1985).

  • S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case. An all-atom force field for simulations of proteins and nucleic acids. J. Computat. Chem. 7, 230-252 (1986). [This paper has been cited more than 3000 times, according to the ISI Web of Science.]

  • L. Noodleman, D. A. Case and A. Aizman. Broken symmetry analysis of spin coupling in iron-sulfur clusters. J. Am. Chem. Soc. 110, 1001-1005 (1988).

  • J.M. Moore, D. A. Case, W.J. Chazin, G.P. Gippert, R. Powls, and P.E. Wright. Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus. Science 240, 314-317 (1988).

  • P. Yip and D.A. Case. A new method for refinement of macromolecular structures based on nuclear Overhauser effect spectra. J. Magn. Reson. 83, 643-648 (1989).

  • M.S. Lee, G.P. Gippert, K.V. Soman, D.A. Case and P.E. Wright. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635-637 (1989). [This paper has been cited more than 375 times, according to the ISI Web of Science.]

  • J. Kottalam and D.A. Case. Langevin modes of macromolecules: application to crambin and DNA hexamers. Biopolymers, 29, 1409-1421 (1990).

  • K. Osapay and D.A. Case. A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113, 9436-9444 (1991).

  • A.G. Palmer, III and D.A. Case. Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 114, 9059-9067 (1992).

  • J.J. Love, X. Li, D.A. Case, K. Giese, R. Grosschedl and P.E. Wright. DNA recognition and bending by the architectural transcription factor LEF-1: NMR structure of the HMG domain complexed with DNA. Nature 376, 791-795 (1995).

  • K. Osapay, W. Young, C.L. Brooks, III, D. Bashford and D.A. Case. Dielectric continuum models for hydration effects on peptide conformational transitions. J. Phys. Chem. 100, 2698-2705 (1996).

  • P. Beroza and D.A. Case. Including sidechain flexibility in continuum electrostatic calculations of protein titrations. J. Phys. Chem. 100, 20156-20163 (1996).

  • W.H. Richardson, C. Peng, D. Bashford, L. Noodleman and D.A. Case. Incorporating solvation effects into density functional theory: Calculation of absolute acidities. Int. J. Quant. Chem. 61, 207-217 (1997)

  • D.A. Case. Calibration of ring current effects in proteins and nucleic acids. J. Biomol. NMR 6, 341-346 (1995).

  • D. Sitkoff and D.A. Case. Density functional calculations of proton chemical shifts in model peptide systems. J. Am. Chem. Soc. 119, 12262-12273 (1997).

  • M.V. Botuyan, A. Toy-Palmer, J. Chung, R.C. Blake, II, D.A. Case and H.J. Dyson. NMR solution structure of Cu(I) rusticyanin from Thiobacillus ferrooxidans: Structural basis for the extreme acid stability and redox potential. J. Mol. Biol. 263, 752-767 (1996).

  • J.A. Smith, L.G. Paloma, D.A. Case, K.C. Nicolaou and W.J. Chazin. Molecular dynamics docking driven by NMR derived restraints to determine the structure of the calicheamicin `gamma sub 1 sup I` oligosaccharide domain complexed to duplex DNA. Magn. Reson. Chem. 34, S147-S155 (1996).

  • P.S. Eis, J.A. Smith, J.M. Rydzewski, D.A. Case, D.L. Boger and D.A. Case. High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. J. Mol. Biol. 272, 237-252 (1997).

  • M.P. Foster, D.S. Wuttke, I. Radhakrishnan, D.A. Case, J.M. Gottesfeld and P.E. Wright. Domain packing and dynamics in the DNA complex of the amino-terminal zinc fingers of transcription factor IIIA. Nature Structural Biology 4, 605-608 (1997).

  • D.S. Wuttke, M.P. Foster, D.A. Case, J.M. Gottesfeld and P.E. Wright. Solution structure of the first three fingers of TFIIIA bound to the cognate DNA sequence: Determinants of affinity and sequence specificity. J. Mol. Biol.273, 183-206 (1997).

  • J. Srinivasan, T.E. Cheatham, III, P. Cieplak, P.A. Kollman and D.A. Case. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120, 9401-9409 (1998).

  • T. Macke and D.A. Case. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids, N.B. Leontes and J. SantaLucia, Jr., eds. (Washington, DC: American Chemical Society, 1998), pp. 379-393.

  • J. Srinivasan, M.W. Trevathan, P. Beroza and D.A. Case. Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects. Theor. Chem. Accts. 101, 426-434 (1999).

  • J. Li, L. Noodleman and D.A. Case. Electronic structure calculations: Density functional methods with applications to transition metal complexes. In Inorganic Electronic Structure and Spectroscopy. Volume 1: Methodology, E.I. Solomon and A.B.P. Lever, eds. (New York: John Wiley, 1999), pp. 661-724.

  • H. Kuramochi, L. Noodleman and D.A. Case. Density functional study on the electronic structures of models for heme peroxidase compounds I and II. J. Am. Chem. Soc. 119, 11442-11451 (1997).

  • A. Dejaegere and D.A. Case. Density functional study of ribose and deoxyribose chemical shifts. J. Phys. Chem. 102, 5280-5289 (1998).

  • D.A. Case. Use of chemical shifts and their anisotropies in biomolecular structure determination. Curr. Opin. Struct. Biol. 8, 624-630 (1998).

  • A.P. Dejaegere, R.A. Bryce and D.A. Case. An empirical analysis of proton chemical shifts in nucleic acids. In Modeling NMR Chemical Shifts, J.C. Facelli and A.C. de Dios, eds. (Washington, American Chemical Society, 1999), pp. 194-206.

  • D.A. Case. Calculations of NMR dipolar coupling strengths in model peptides. J. Biomol. NMR 15, 95-102 (1999).

  • G.P. Gippert, P.E. Wright and D.A. Case. Recursive torsion angle grid search in high dimensions: A systematic approach to NMR structure determination. J. Biomol. NMR 11, 241-263 (1998).

  • Y. Chen, D.A. Case, J. Reizer, M.H. Saier, Jr. and P.E. Wright. High resolution structure of Bacillus subtilis IIAglc. Proteins 31, 258-270 (1998).

  • V. Tsui, L. Zhu, T.-H. Huang, P.E. Wright and D.A. Case. Assessment of zinc finger orientations by residual dipolar coupling constants. J. Biomol. NMR 16, 9-21 (2000).

  • G.B. Legge, R.W. Kriwacki, J. Chung, U. Hommel, P. Ramage, D.A. Case, H.J. Dyson and P.E. Wright. NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. J. Mol. Biol. 295, 1251-1264 (2000).

  • J.A. Smith, G. Bifulco, D.A. Case, D.L. Boger, L. Gomez-Paloma and W.J. Chazin. The structural basis for in situ activation of DNA alkylation by duocarmycin SA. J. Mol. Biol. 300, 1195-1204 (2000).

  • V. Tsui, I. Radhakrishnan, P.E. Wright and D.A. Case. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. J. Mol. Biol. 302, 1101-1117 (2000).

  • D. Bashford and D.A. Case. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51, 129-152 (2000).

  • A. Onufriev, D. Bashford and D.A. Case. A modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. 104, 3712-3720 (2000).

  • V. Tsui and D.A. Case. Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J. Am. Chem. Soc. 122, 2489-2498 (2000).

  • A.K. Ogawa, O.K. Abou-Zied, V. Tsui, R. Jimenez, D.A. Case and F.E. Romesberg. A photo-tautomerizable model DNA base pair. J. Am. Chem. Soc. 122, 9917-9920 (2000).

  • M.S. VanLoock, A. Malhotra, D.A. Case, R. Agrawal, P. Penczek, T.R. Easterwood, J. Frank and S.C. Harvey, "A functional interpretation of the cryo-electron microscopy map of the 30S ribosomal subunit from Escherichia coli. In The Ribosome: Structure, Function, Antibiotics and Cellular Interactions, R.A. Garrett, S.R. Douthwaite, A. Liljas, A.T. Matheson, P.B. Moore and H.F. Noller, eds. (Washington, DC: ASM Press, 2000), pp. 165-171.

  • D.A. Case, L. Noodleman and J. Li. Modern computational approaches to modeling polynuclear transition metal complexes. In Metal-Ligand Interactions in Physics, Chemistry and Biology, N. Russo and D.R. Salahub, eds. (Dordrecht: Kluwer, 2000), pp. 19-47.

  • G. Cornilescu, A. Bax and D.A. Case. Large variations in one-bond 13Cα-13Cβ J couplings in polypeptides correlate with backbone conformation. J. Am. Chem. Soc. 122, 2168-2171 (2000).

  • D.A. Case, C. Scheurer and R. Brüschweiler. Density functional calculations of scalar 3J couplings in peptides and proteins. J. Am. Chem. Soc. 122, 10390-10397 (2000).



    Updated on August 16, 2017. Comments to case@biomaps.rutgers.edu