Some of my earlier papers that are still of greatest interest are listed
here.
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.
D.A. Case. Use of chemical shifts and their anisotropies in biomolecular
structure determination. Curr. Opin. Struct. Biol. 8, 624-630
(1998).
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).
D. Bashford and D.A. Case. Generalized Born models of macromolecular
solvation effects. Annu. Rev. Phys. Chem. 51, 129-152 (2000).
J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv.
Prot. Chem. 66, 27-85 (2003).
D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz,
Jr., A.
Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular
simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).
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).
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).
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).
J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman and D.A. Case. Development
and testing of a general Amber force field. J. Comput. Chem. 25,
1157-1174 (2004).
J. Wang, W. Wang, P.A. Kollman and D.A. Case.
Automatic atom type and bond type perception in molecular mechanical
calculations. J. Mol. Graphics.
Model. 25, 247-260 (2006).
T. Steinbrecher, D.L. Mobley and D.A. Case. Non-linear scaling
schemes for Lennard-Jones interactions in free energy calculations. J. Chem.
Phys. 127, 214018 (2007).
R.C. Walker, M.F. Crowley and D.A. Case. The implementation of a fast
and accurate QM/MM potential method in Amber. J. Comput. Chem. 28,
1019-1031 (2008).
T. Steinbrecher, I.S. Joung and D.A. Case. Soft-core potentials in
thermodynamic integration - Comparing one- and two-step transformations. J.
Comput. Chem. 32, 3253-3263 (2011).
Updated on November 20, 2023. Comments to david.case@rutgers.edu