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).
P.F. Batcho, D.A. Case, and T. Schlick. Optimized particle-mesh
Ewald/multiple-timestep integration for molecular dynamics simulations
J. Chem. Phys. 115, 4003-4018 (2001).
P.A. Kollman and D.A. Case. Drug-target binding forces: Advances in
force field approaches. Burger's Medicinal Chemistry, Sixth Edition. Vol.
1: Drug Discovery. D.J. Abraham, Ed. (New York, John Wiley & Sons, 2003),
pp. 169-185.
D. A. Case and D. R. Herschbach. Statistical theory
of angular momentum polarization in chemical reactions. Mol. Phys.
100, 109-125 (2002). [This is a reprinted version of a 1975 paper,
chosen as one of the most significant papers of the first 100 issues of
Molecular Physics. See also the commentary by D.C. Cleary: Mol.
Phys. 100, 107 (2002).]
H. Liu, C. Qu, J.E. Johnson and D.A. Case. Pseudo-atomic models of
swollen
CCMV from cryo-electron micrscopy data. J. Struct. Biol. 142,
356-363 (2003).
J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv.
Prot. Chem. 66, 27-85 (2003). (Illustration shows a solvated free
energy surface for the alanine dipeptide.)
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).
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).
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).
F. Paesani, W. Zhang, D.A. Case, T.E. Cheatham III, and G.A. Voth.
An accurate and simple quantum model for liquid water. J. Chem. Phys.
125, 184507 (2006).
G.M. Seabra, R.C. Walker, M. Elstner, D.A. Case, and A.E. Roitberg.
Implementation of the SCC-DFTB method for hybrid QM/MM simulations
within the Amber molecular dynamics package. J. Phys. Chem. A 111,
5655-5664 (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, 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).
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. Onufriev, D.A. Case and G.M. Ullmann. A novel view of pH titration
in biomolecules. Biochemistry 40, 3413-3419 (2001).
C.P. Sosa, T. Hewitt, M.S. Lee and D.A. Case. Vectorization of the
generalized Born model for molecular dynamics on shared-memory computers.
J. Mol. Struct. (Theochem) 549, 193-201 (2001).
V. Tsui and D.A. Case. Theory and applications of the generalized Born
solvation model in macromolecular simulations. Biopolymers: Nucleic
Acid Sciences 56, 275-291 (2001).
A. Onufriev, D.A. Case and D. Bashford. Effective Born radii in the
generalized Born approximation: The importance of being perfect. J.
Computat. Chem. 23, 1297-1304 (2002).
M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case and C.L. Brooks, III.
Performance comparison of generalized Born and Poisson methods in the
calculation of electrostatic solvation energies for protein structures.
J. Comput. Chem. 25, 265-284 (2004).
A. Onufriev, D. Bashford and D.A. Case. Exploring protein native states and
large-scale conformational changes with a modified generalized Born model.
Proteins 55, 383-394 (2004).
T. Simonson, J. Carlsson and D.A. Case. Proton binding to proteins:
pKa calculations with explicit and implicit solvent models. J. Am. Chem.
Soc. 126, 4167-4180 (2004).
V. Roberts, D.A. Case, and V. Tsui. Predicting interactions of winged-helix
transcription factors with DNA. Proteins 57, 172-87 (2004).
(Illustration at right shows the protein/DNA binding
motif)
J. Mongan, D.A. Case and J.A. McCammon. Constant pH molecular dynamics in
generalized Born implicit solvent. J. Comput. Chem. 25, 2038-2048
(2004).
J. Mongan and D.A. Case. Biomolecular simulations at constant pH.
Curr. Opin. Struct. Biol. 15, 157-163 (2005).
R.C. Rizzo, T. Aynechi, D.A. Case and I.D. Kuntz. Estimation of absolute
free
energies of hydration using continuum methods: Accuracy of partial charge
models and optimization of nonpolar contributions. J. Chem. Theory
Comput. 2, 128-139 (2006).
N.A. Baker, D. Bashford and D.A. Case. Implicit solvent electrostatics in
biomolecular simulation. In New Algorithms for Macromolecular
Simulation, B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark,
T. Schlick, C. Schütte, and R. Skeel, eds. (New York: Springer-Verlag, 2006),
pp. 263-295.
R.A. Brown and D.A. Case. Second derivatives in generalized Born theory.
J. Comput. Chem. 27, 1662-1675 (2006).
J. Mongan, C. Simmerling, J.A. McCammon, D.A. Case, and A. Onufriev.
Generalized Born model with a simple, robust molecular volume
correction. J. Chem. Theory Comput. 3, 156-169 (2007).
W. Cornell, R. Abseher, M. Nilges and D.A. Case. Continuum solvent
molecular dynamics study of flexibility in interleukin-8. J. Mol.
Graphics Model. 19, 136-145 (2001).
R. Jimenez, D.A. Case and F.E. Romesberg. Flexibility of an
antibody binding site measured with photon echo
spectroscopy. J. Phys. Chem. B106, 1090-1103 (2002).
A. Onufriev, D.A. Case and D. Bashford. Structural details, pathways, and
energetics of unfolding of apomyoglobin. J. Mol. Biol. 325, 555-567
(2003).
H. Gohlke, C. Kiel, and D.A. Case. Insights into protein-protein binding by
binding free energy calculation and free energy decomposition for the Ras-Raf
and Ras-RalGDS complexes. J. Mol. Biol. 330, 891-913 (2003).
H. Gohlke, L. Kuhn and D.A. Case. Change in flexibility upon complex
formation: Analysis of Ras-Raf using molecular dynamics and a molecular
framework approach. Proteins 56, 322-337 (2004). (Illustration
shows the graph model used in the FIRST molecular framework
approach)
H. Gohlke and D.A. Case. Converging free energy estimates: MM-PB(GB)SA
studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25,
238-250 (2004).
T. Steinbrecher, D.A. Case and A. Labahn. A multistep approach to
structure
based drug design: Studying ligand binding at the human neutrophil elastase.
J. Med. Chem. 49, 1837-1844 (2006).
R.J. Payne, S. Ficht, S. Tang, A. Brik, Y.-Y. Yang, D.A. Case and
C.-H Wong. Extended sugar-assisted glycopeptide ligations: Development, scope
and application. J. Am. Chem. Soc. 129, 13527-13536 (2007).
F.Y. Dupradeau, S. Pissard, M.P. Coulhon, E. Cadet, K. Foulon, C.
Fourcade, M. Goossens, D.A. Case, and J. Rochette. An unusual compound
heterozygosity in HFE Hemochromatosis (p.G43D-H63D/p.C282Y): a
computationally-based study of the cis mutations with implication in
binding to transferrin receptor 1. Human Mutation 29, 206 (2008).
A.P. Graves, D.M. Shivakumar, S.E. Boyce, M.P. Jacobson, D.A. Case
and B. Shoichet. Rescoring docking hit lists for model cavity sites:
predictions and experimental testing. J. Mol. Biol. 377, 914-934
(2008).
T. Hou, W. Zhang, D.A. Case, and W. Wang. Deciphering the binding
patterns of the peptide ligands of amphiphysin-1 SH3 domain by analyzing the
molecular interaction fields. J. Mol. Biol. (in press).
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.
V. Tsui and D.A. Case. Calculations of the absolute free energies of
binding
between RNA and metal ions using molecular dynamics simulations and
continuum electrostatics. J. Phys. Chem. B 105, 11314-11325 (2001).
T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case and R. Sampath.
RNAMotif: A new RNA secondary structure definition and discovery algorithm.
Nucl. Acids Res. 29, 4724-4735 (2001).
A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret, S.C.
Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker and F. Major. RNAML:
A standard syntax for exchanging RNA information. RNA 8, 707-717
(2002).
H. Gouda, I.D. Kuntz, D.A. Case and P.A. Kollman. Free energy calculations
for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and
thermodynamic integration methods. Biopolymers 68, 16-34 (2003).
V. Tsui, T. Macke, and D.A. Case. A novel method for finding tRNA
genes. RNA 9, 507-517 (2003). (Figure shows a "descriptor" for
finding tRNA genes in prokaryotes.)
H.T. Allawi, M.W. Kaiser, A.V. Onufriev, W.-P. Ma, A.E. Brogard, D.A.
Case,
B.P. Neri and V.I Lyamichev. Modeling of flap endonuclease interactions with
DNA substrate. J. Mol. Biol. 328, 537-554 (2003).
D.L. Beveridge, G. Barreiro, S. Byun, D.A. Case, T.E. Cheatham, III, S.B.
Dixit, E. Giudice, F. Lankas, R. Lavery, J. Maddocks, R. Osman, H. Sklenar, G.
Stoll, K.M. Thayer, P. Varnai and M.A. Young. Molecular dynamics simulations
of the 136 tetranucleotide sequences of DNA oligonucleotides. I. Research
design, informatics, and results on d(CpG) steps. Biophys. J.
87, 3799-3813 (2004).
S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham, III, E. Giudice,
F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, H. Sklenar, K.M. Thayer,
and P. Varnai.
Molecular dynamics simulations of the 136 unique tetranucleotide sequences
of DNA oligonucleotides. II. Sequence context effects on the dynamical
structures of the 10 unique dinucleotide steps.
Biophys. J. 89, 3721-3740 (2005).
F.-Y. Dupradeau, D.A. Case, C. Yu, R. Jimenez and F.E. Romesberg.
Differential solvation and tautomer stability of a model base pair withing the
minor and major groove of DNA. J. Am. Chem. Soc. 127, 15612-15617
(2005).
T.E. Cheatham, III and D.A. Case. Using Amber to simulate
DNA and RNA. In Computational Studies of DNA and RNA, J.
Sponer and F. Lankas, eds. (Dordrecht: Springer, 2006), pp 45-72.
D.H. Mathews and D.A. Case. Nudged Elastic Band calculation of minimal
energy
pathways for the conformational change of a GG mismatch. J. Mol. Biol.
357, 275-291 (2006).
Q. Cui, R.K.-Z. Tan, S.C. Harvey and D.A. Case. Low-resolution molecular
dynamics simulations of the 30S ribosomal subunit. Multiscale Model. Simul.
5, 1248-1263 (2006).
R.K. Grover, S.J. Pond, Q. Cui, P. Subramaniam, M. Puga, D.A. Case, D.P.
Millar and P. Wentworth, Jr. O-Glycoside orientation is an essential aspect
of base J recognition by the kinetoplastid DNA-binding protein JBP1.
Angew. Chemie 46, 2839-2843 (2007).
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.
T. Lovell, J. Li, T. Liu, D.A. Case and L. Noodleman. FeMo cofactor of
nitrogenase: A density functional study of states MN, MOX,
MR and MI. J. Am. Chem. Soc. 123, 12392-12410 (2001).
G.M. Ullmann, L. Noodleman and D.A. Case. Density functional
calculation of the pKa values and redox potentials in the bovine
Rieske iron-sulfur protein. J. Biol. Inorg. Chem. 7, 623-639 (2002).
T. Lovell, J. Li, D.A. Case and L. Noodleman. FeMo cofactor of
nitrogenase:
Energetics and local interactions in the protein environment. J. Biol.
Inorg. Chem. 7, 735-749 (2002).
T. Lovell, J. Li, D.A. Case and L. Noodleman. Binding modes for the
first coupled electron and proton addition to FeMoco of nitrogenase. J. Am.
Chem. Soc. 124, 4546-4547 (2002).
T. Lovell, R.A. Torres, W.-G. Han, T. Liu, D.A. Case and L. Noodleman. Metal
substitution in the active site of nitrogenase MFe7S9
(M=Mo4+, V3+, Fe3+. Inorg. Chem 41, 5744-5753
(2002).
R.A. Torres, T. Lovell, L. Noodleman and D.A. Case. Density functional and
reduction potential calculations of Fe4S4 clusters. J. Am.
Chem. Soc. 125, 1923-1936 (2003).
J.A. Fee, J.M. Catagnetto, D.A. Case, L. Noodleman, C.D. Stout and R.A.
Torres. The circumsphere as a tool to assess distortion in [4Fe-4S] atom
clusters. J. Biol. Inorg. Chem. 8, 519-526 (2003). (Figure shows a
geometric analysis of these cubane systems.)
R.-J. Cheng, P.-Y. Chen, T. Lovell, T. Liu, L. Noodleman and D.A. Case.
Symmetry and bonding in metalloporphyrins. A modern implementation for the
bonding analyses of five- and six-coordinate high-spin iron(III) porphyrin
complexes through density functional calculation and NMR spectroscopy.
J. Am. Chem. Soc. 125, 6774-6783 (2003).
Y. Xiao, M. Koutmos, D.A. Case, D. Coucouvanis, H. Wang and S.P. Cramer.
Dynamics of an [Fe4S4(SPh)4]2- cluster via IR,
Raman, and nuclear resonant vibrational spectroscopy (NRVS). Analysis using
36S substitution, DFT and empirical force fields. J. Chem. Soc.
Dalton, 2192-2201 (2006).
Y. Xiao, K. Fisher, M.C. Smith, W.E. Newton, D.A. Case, S.J. George, H.
Wang,
W. Sturhahn, E.E. Alp, J. Zhao, Y. Yoda and S.P. Cramer. How nitrogenase
shakes--initial information about P-cluster and FeMo-cofactor normal modes
from nuclear resonance vibrational spectroscopy (NRVS). J. Am. Chem.
Soc. 128, 7608-7612 (2006).
D. Lukoyanov, V. Pelmenschikov, N. Maeser, M. Laryukhin, T.C. Yang,
L. Noodleman, D.R. Dean, D.A. Case, L.C. Seefeldt, and B.M. Hoffman. Testing
if the interstitial atom, X, of the nitrogenase molybdenum-iron cofactor is N
or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 resting state in multiple
environments. Inorg. Chem. 46, 11437-11439 (2007).
Y. Guo, H. Wang, Y. Xiao, S. Vogt, R.K. Thauer, S. Shima, P.I.
Volkers, T.B. Rauchfuss, V. Pelmentschikov, D.A. Case, E.E. Alp, W. Sturhahn,
Y. Yoda, and S.P. Cramer. Characterization of the Fe Site in
Methanothermobacter marburgensis Hydrogenase (mHmd) and a Model Compound via
Nuclear Resonance Vibrational Spectroscopy (NRVS). Inorg. Chem. (in press).
D.S. Wishart and D.A. Case. Use of chemical shifts in macromolecular
structure determination. Meth. Enzymol. 338, 3-34 (2001).
X.P. Xu and D.A. Case. Automated prediction of 15N,
13C`alpha`, 13C`beta` and 13C' chemical shifts in proteins
using a density functional database. J. Biomol. NMR 21 321-333
(2001).
X.P. Xu and D.A. Case. Probing multiple effects on 15N,
13C`alpha`, 13C`beta` and 13C' chemical shifts in peptides
using density functional theory. Biopolymers 65, 408-423 (2002).
(Figure shows some effects of hydrogen bonds on heavy
atoms shifts in peptides)
S. Moon and D.A. Case. A comparison of quantum chemical models for
calculating NMR shielding parameters in peptides : Mixed-basis-set and ONIOM
methods
combined with a complete basis-set extrapolation. J. Comput. Chem.
27, 825-836 (2006).
S. Moon and D.A. Case. A new model for chemical shifts of amide hydrogens
in proteins. J. Biomol. NMR 138, 139-150 (2007).
S. Tang and D.A. Case. Vibrational averaging of chemical shift
anisotropies in model peptides. J. Biomol. NMR. 38, 255-266 (2007).
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).
D.A. Case. Interpretation of chemical shifts and coupling constants in
macromolecules. Curr. Opin. Struct. Biol. 10, 197-203 (2000).
G. Cornilescu, A. Bax and D.A. Case. Large variations in one-bond
13C`alpha`-13C`beta` 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.J. Chou, D. Case and A. Bax. Insights in mobility of methyl-bearing
sidechains in proteins from 3JCC and 3JCN couplings.
J. Am. Chem. Soc. 125, 8959-8966 (2003).
D.A. Case. Molecular dynamics and NMR spin relaxation in proteins.
Acc. Chem. Res. 35, 325-331 (2002).
B. Xia, V. Tsui, D.A. Case, H.J. Dyson and P.E. Wright. Comparison of
protein
solution structures refined in vacuum, with a generalized Born model, and
with explicit water. J. Biomol. NMR 22, 317-331 (2002).
L. Moulinier, D.A. Case and T. Simonson. Re-introducing electrostatics into
protein X-ray structure refinement: bulk solvent treated as a dielectric
continuum. Acta Cryst. D 59, 2094-2103 (2003). (Figure shows a
piece of X-ray density using an implicit solvent refinement model.)
M.F. Roberts, Q. Cui, C.J. Turner, D.A. Case and A.G. Redfield. High
resolution field-cycling NMR studies of a DNA octamer as a probe of
phosphodiester dynamics, and comparisons with computer simulation.
Biochemistry 43, 3637-3650 (2004).
V. Wong and D.A. Case. Evaluating rotational diffusion from protein MD
simulations. J. Phys. Chem. B, (in press,
asap).
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).
M.V. Botuyan, G. Mer, G.-S. Yi, C.M. Koth, D.A. Case, A.M. Edwards, W.J.
Chazin and C.H. Arrowsmith. Solution structure and dynamics of yeast
elongin C in complex with a von Hippel-Lindau peptide. J. Mol. Biol.
312, 177-186 (2001).
Q. Zhang, T. Dwyer, V. Tsui, D. Case, J. Cho, P.B. Dervan and D.E. Wemmer.
NMR structure of a cyclic polyamide-DNA complex. J. Am. Chem. Soc.
126, 7958-7966 (2004). (Figure shows a superposition of NMR structures
for this complex.)
B.M. Lee, J. Xu, B.K. Clarkson, M.A. Martinez-Yamout, H.J. Dyson, D.A.
Case,
J.M. Gottesfeld, and P.E. Wright. Induced fit and "lock and key" recognition
of 5S RNA by zinc fingers of transcription factor IIIA. J. Mol. Biol.
357, 275-291 (2006).
J. Chen, F.-Y. Dupradeau, D.A. Case, C.J. Turner and J. Stubbe. NMR
structural studies and molecular modeling of duplex DNA containing normal and
4'-oxidized abasic sites. Biochemistry 46, 3096-3107 (2007).
221. J. Chen, F.-Y. Dupradeau, D.A. Case, C.J. Turner and J. Stubbe. DNA
oligonucleotides with A, T, G, or C opposite an abasic site: Structure and
dynamics. Nucl. Acid Res. 36, 253-262 (2008).
Updated on April 17, 2008. Comments to case@scripps.edu