You can also visit my
Google Scholar
profile for information about publications. Same thing,
sorted by year of publication, i.e. to see my recent publications.)
R. Salomon-Ferrer, D.A. Case and R.C. Walker. An overview of the
Amber biomolecular simulation package. WIREs: Comput. Mol. Sci. 3,
198-210 (2013).
(Figure shows the cover of the Amber Users'
Manual)
J. Latzer, T. Steinbrecher and D.A. Case. Revised AMBER parameters
for bioorganic phosphates. J. Chem. Theory Comput. 8, 4405-4412 (2012).
D.S. Cerutti, J.E. Rice, W. Swope, and D.A. Case. Derivation of fixed
partial charges for amino acid analogs accommodating a specific water model
and implicit polarization. J. Phys. Chem. B 117, 2328-2338 (2013).
D.S. Cerutti, W.C. Swope, J.E. Rice and D.A. Case. ff14ipq: A
self-consistent force field for condensed-phase simulations of proteins. J.
Chem. Theory Comput. 10, 4515-4534 (2014).
I. Ivani, P.D. Dans, A. Noy, A. Pérez, I. Faustino, A. Hopsital, J.
Walther, P. Andrió, R. Goñi, A. Balaceanu, G. Portella, F. Battistini, J.L.
Gelpí, C. González, M. Vendruscolo, C.A. Laughton, S. Harris, D.A. Case and
M. Orozco. Parmbsc1: A refined force field for DNA simulations. Nature
Methods 13, 55-58 (2016).
K.T. Debiec, D.S. Cerutti, L.R. Baker, A.M. Gronenborn, D.A. Case,
and L.T. Chong. Further along the Road Less Traveled: AMBER ff15ipq, an
Original Protein Force Field Built on a Self-Consistent Physical Model. J.
Chem. Theory Comput. 12, 3926-3947 (2016).
Y. Hu, B. Sherborne, T.-S. Lee, D.A. Case, D.M. York and Z. Guo.
Predicting relative binding affinity with workflow approaches: a comparison of
AMBER TI and Schrödinger FEP.J. Comput. Aided Mol. Des. 30, 533-539
(2016).
A. Albaugh, R.T. Bradshaw, O. Demerdash, J. Dziedzic, Y. Mao, D.T.
Margul, J. Swails, H.A. Boateng, D.A. Case, P. Eastman, J.W. Essex, M.
Head-Gordon, V.S. Pande, J. Ponder, Y. Shao, C. Skylaris, I.T. Todorov, M.E.
Tuckerman, Q. Zeng, T. Head-Gordon. Advanced Potential Energy Surfaces for
Molecular Simulation. J. Phys. Chem. B 120, 9811-9821 (2016).
D.S. Cerutti, K.T. Debiec, D.A. Case and L.T. Chong. Links between
the charge model and bonded parameter force constants in biomolecular force
fields. J. Chem. Phys. 147, 161730 (2017).
T.-S. Lee, D.S. Cerutti, D. Mermelstein, C. Lin, S. LeGrand, T.J.
Giese, A. Roitberg, D.A. Case, R.C. Walker, and D.M. York. GPU-accelerated
molecular dynamics and free energy methods in Amber18: performance
enhancements and new features. J. Chem. Inf. Model. 58, 2043-2050 (2018).
A.B. Rubenstein, K. Blacklock, H. Nguyen, D.A. Case and S.D. Khare.
Systematic comparison of Amber and Rosetta energy functions for protein
structure evaluation. J. Chem. Theory Comput. 14, 6015-6025
(2018).
A.T. Bogetti, H.E. Piston, J.M. G. Leung, C.C. Cabalteja, D.T.
Yang, A.J. DeGrave, K.T. Debiec, D.S. Cerutti, D.A. Case, W.S. Horne,
and L.T. Chong. A Twist in the Road Less Traveled: The AMBER ff15ipq-m
Force Field for Protein Mimetics. J. Chem. Phys. 153, 064101 (2020).
D.A. Case, H.M. Aktulga, K. Belfon, D. Cerutti, G.A. Cisneros,
V.W. Cruzeiro, N. Forouzesh, T. Giese, A. Götz, H. Gohlke, S. Izadi, K.
Kasavajhala, M. Kaymak, E. King, T. Kurtzman, T. Lee, P. Li, J. Liu, T.
Luchko, R. Luo, M. Machado, M. Manathunga, H. Nguyen, K. O'Hearn, A.
Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S.
Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S.
Zhang, S. Zhao, Q. Zhu, T. Cheatham, D.R. Roe, A. Roitberg, C.
Simmerling, D. York, M. Nagan, and K. Merz. AmberTools. J. Comput. Inf.
Model. 63, 6183-6191 (2023).
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.)
D.S. Cerutti, P.L. Freddolino, R.E. Duke, Jr. and D.A. Case. Simulations
of a protein crystal with a high resolution X-ray structure:
Evaluation of force fields and water models. J. Phys. Chem. B 114,
12811-12824 (2010).
P.A. Janowski, D.S. Cerutti, J. Holton and D.A. Case. Peptide crystal
simulations reveal hidden dynamics. J. Am. Chem. Soc. 135, 7938-7948
(2013).
X. Wu, S. Subramaniam, D.A. Case, K. Wu and B.R. Brooks. Map
constrained self-guided Langevin dynamics. J. Struct. Biol. 183,
429-440 (2013).
H. Nguyen, S.A. Pabitt, S. Meisburger, L. Pollack and D.A. Case.
Accurate small and wide angle X-ray scattering profiles from atomic models of
proteins and nucleic acids. J. Chem. Phys. 114, 22D508 (2014).
C. Liu, P.A. Janowski and D.A. Case. All-atom crystal simulations of
DNA and RNA duplexes. Biochim. Biophys. Acta 1850, 1059-1071 (2015).
P.A. Janowski, C. Liu and D.A. Case. Molecular dynamics of triclinic
lysozyme in a crystal lattice. Prot. Sci. 25, 87-102 (2016).
H.T. Nguyen, S.A. Pabit, L. Pollack and D.A. Case. Extracting water
and ion distributions from small angle X-ray scattering experiments. J. Chem.
Phys. 144, 214105 (2016).
P.A. Janowski, N.W. Moriarty, B.P. Kelly, D.A. Case, D.M. York, P.D.
Adams and G.L. Warren. Phenix-AFITT: Improved ligand geometries in
crystallographic refinement using AFITT in Phenix. Acta Cryst. D 72,
1062-1072 (2016).
K. Zhang, S. Keane, Z. Su, R.N. Irobalieva, M. Chen, J. Marchant, X.
Heng, M.F. Schmid, D.A. Case, S.J. Ludtke, M.F. Summers and W. Chiu. Structure
of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid of CryoEM, NMR and
Molecular Dynamics. Structure 26, 490-498 (2018).
D.S. Cerutti and D.A. Case. Molecular dynamics simulations of
macromolecular crystals. Wires Comput. Mol. Sci. e1402, (2018).
N.W. Moriarty, P.A. Janowski, J.M. Swails, H. Nguyen, J.S.
Richardson, D.A. Case and P.D. Adams. Improved chemistry restraints for
crystallographic refinement by integrating Amber molecular mechanics
into Phenix. Acta Cryst. D76, 51-62 (2020).
S.P. Meisburger, D.A. Case and N. Ando. Correlated motions in a
protein crystal. Nature Commun. 11, 1271 (2020).
J.G. Gray and D.A. Case. Refinement of RNA structures guided by
the Amber force field. Crystals 11, 771 (2021).
S.J. Budiardjo, J.J. Stevens, A.L. Calkins, A.P. Ikujuni, V.K.
Wimalasena, E. Firlar, D.A. Case , J.S. Biteen, J.T. Kaelber and J.S.G.
Slusky. Colicin E1 binds to TolC as an open hinge to penetrate the
outer-membrane. eLife 11, e73297 (2022).
S.P. Meisburger, D.A. Case and N. Ando. Robust total X-ray
scattering workflow to study correlated motion of proteins in crystals.
Nature Commun. 14, 1228 (2023).
D.A. Case. MD Simulations of macromolecular crystals:
Implications for the analysis of Bragg and diffuse scattering. Meth.
Enzymol. 688, 145-168 (2023).
O. Mikhailovskii, S.A. Izmailov, Y. Xue, D.A. Case, and N.R.
Skrynnikov. X-ray crystallography module in the Amber 2023 simulation
program. Refining the models of protein crystals. J. Comput. Inf. Model.
64, 18-25 (2024).
V. Wong, D.A. Case and A. Szabo. Influence of the coupling of interdomain
and overall motions on NMR relaxation. Proc. Natl. Acad. Sci. USA
101, 11016-11021 (2009).
B.S. Tolbert, Y. Miyazaki, S. Barton, B. Kinde, P. Starck, R. Singh,
A. Bax, D.A. Case,
and M.F. Summers. Major groove width variations in RNA structures
determined by NMR and impact of 13C residual chemical shift anisotropy and
1H--13C residual dipolar coupling on refinement. J. Biomol.
NMR 47, 205-219 (2010).
J. Xia, C.J. Margulis and D.A. Case. Searching and optimizing
structure ensembles for complex flexible sugars. J. Am. Chem. Soc.
133, 15252-15255 (2011). (Figure shows some selected
ensembles of simple sugars.)
J. Xia and D.A. Case. Sucrose in aqueous solution revisited. 1.
Molecular dynamics simulations and direct and indirect dipolar coupling
analysis. Biopolymers, 97, 276-288 (2012).
J. Xia and D.A. Case. Sucrose in aqueous solution revisited. 2.
Adaptively biased molecular dynamics simulations and computational analysis of
NMR relaxation. Biopolymers, 97, 289-302 (2012).
H. Zhang, G. Hou, M. Lu, J. Ahn, I.-J. Byeon, C.J. Langmead, J.R.
Perilla, I. Hung, P.L. Gor’kov, Z. Gan, W. Brey, D.A. Case, K. Schulten, A.M.
Gronenborn, and T. Polenova. HIV-1 Capsid Function is Regulated by Dynamics:
Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning
NMR, QM/MM, and MD. J. Am. Chem. Soc. 138, 14066-14075 (2016).
D.A. Case and N.R. Skrynnikov. Interview with David A. Case: on force
fields, biomolecular modeling, and NMR. Concepts Magn. Reson.
Part A e21403 (2018).
H. Nam, O. Becette, R.M. LeBlanc, D.S. Oh, D.A. Case, and T.K.
Dayie. Deleterious effects of carbon-carbon dipolar coupling on RNA NMR
dynamics. J. Biomol. NMR 74, 321-331 (2020).
E. Zuiderweg and D.A. Case. New experimental evidence for
pervasive dynamics in proteins. Prot. Sci. 32, e4630 (2023).
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.)
G.M. Giambasu, D.M. York and D.A. Case. Structural fidelity and NMR
relaxation analysis in a prototype RNA hairpin. RNA 21, 963-974 (2015).
S.C. Keane, X. Heng, K. Lu, S. Kharytonchyk, V. Ramakrishnan, G.
Carter, S. Barton, A. Hosic, A. Florwick, J. Santos, N. Bolden, S. McCowin,
D.A. Case, B. Johnson, M. Salemi, A. Telesnitsky, and M.F. Summers. Structure
of the HIV-1 RNA packaging signal. Science, 348, 917-921 (2015).
L. Salmon, G.M. Giambasu, E.N. Nikolova, K. Petzold, A.
Bhattacharya, D.A. Case and H.M. Al-Hashimi. Modulating RNA Alignment Using
Directional Dynamic Kinks: Application in Determining an Atomic-Resolution
Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J. Am.
Chem. Soc. 137, 12954-12965 (2015).
C.-H. Hsu, S. Park, D.E. Mortenson, B.L. Foley, R.J. Woods, D.A.
Case, E.T. Powers, C.-H. Wong, H.J. Dyson and J.W. Kelly. The Dependence of
Carbohydrate--Aromatic Interaction Strengths on the Structure of the
Carbohydrate. J. Am. Chem. Soc. 138, 7636-7648 (2016).
J.J. Bouchard, J. Xia, D.A. Case and J.W. Peng. A new approach for
ensemble descriptions of interdomain motions: application to Pin1. J. Mol.
Biol. 430, 2164-2180 (2018).
M. Zhang, D.A. Case, and J.W. Peng. Propagated perturbations from a
peripheral mutation map interactions supporting WW domain thermostability.
Structure 26, 1474-1485 (2018).
J.D. Brown, S. Kharytonchyk, A.S. Iyer, H. Carter, Y. Desai, L.
Glang, S.H. Choi, M.W. Lopresti, I. Chaudry, K. Singh, M. Orellana, T.
Rodriguez, U. Oboh, J. Hijji, F.G. Ghinger, K. Stewart, G. Becker, D.
Francis, B. Edwards, P. Chen, D.A. Case, A. Telesnitsky, and M.F.
Summers. Structural Basis for Transcriptional Start Site Control of
HIV-1 RNA Fate. Science 368, 413–417 (2020).
M. Zhang, T.E. Frederick, D.A. Case, J.W. Peng. Coupled
intra-and interdomain dynamics support domain cross-talk in Pin1. J.
Biol. Chem. 295, 16585-16603 (2020).
H. Shi, A. Rangadurai, H.A. Assi, R. Roy, D.A. Case, D.
Herschlag, J.D. Yesselman, and H.M. Al-Hashimi. Rapid and accurate
determination of atomistic RNA dynamic ensemble models using NMR and
structure prediction. Nature Commun. 11, 5531 (2020).
B. Liu, H. Shi, A. Rangadurai, C.-C. Chu, F. Nussbaumer, K.A.
Erharter, D.A. Case, C. Kreutz, and H.M. Al-Hashimi. m6A delays
base-pairing through syn-anti isomerization of the methylamino group.
Nature Commun. 12, 1-17 (2021).
A. Geng, L. Ganser, R. Roy, S. Pratihar, D.A. Case, and H.M.
Al-Hashimi. An RNA excited conformational state at atomic resolution.
Nature Commun. 14, 8432 (2023).
S. Tang and D.A. Case. Vibrational averaging of chemical shift
anisotropies in model peptides. J. Biomol. NMR. 38, 255-266 (2007).
S. Tang and D.A. Case. Calculation of chemical shift anisotropy in
proteins. J. Biomol. NMR 51, 303-312 (2011).
D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct.
Biol. 23, 172-176 (2013).
J. Swails, T. Zhu, X. He and D.A. Case. AFNMR: Automated fragment
quantum mechanical calculations of chemical shifts in biomolecules. J. Biomol.
NMR 63, 125-139 (2015).
J. Kraus, R. Gupta, J. Yehl, M. Lu, D.A. Case, A.M. Gronenborn, M.
Akke, and T. Polenova. Chemical Shifts of the Carbohydrate Binding Domain of
Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum
Mechanics/Molecular Mechanics Calculations. J. Phys. Chem. B 122,
2931-2939 (2018).
M. Fritz, C.M. Quinn, M. Wang, G. Hou, X. Lu, L.M.I. Koharudin, J.
Struppe, D.A. Case, T. Polenova and A.M. Gronenborn. Accurate determination of
backbone chemical shift tensors in microcrystalline proteins by integrated MAS
NMR and QM/MM. Phys. Chem. Chem. Phys. 20, 9543-9553 (2018).
H. Shi, M.C. Clay, A. Rangadurai, B. Sathyamoorthy, D.A. Case, and
H.M. Al-Hashimi. Atomic Structures of Excited State A-T Hoogsteen Base Pairs
in Duplex DNA by Combining NMR Relaxation Dispersion, Mutagenesis, and
Chemical Shift Calculations. J. Biomol. NMR 70, 229-244 (2018).
H. Zhou, B. Sathyamoorthy, A. Stelling, Y. Xu, Y. Xue, Y.Z.
Pigli, D.A. Case, P.A. Rice, and H.M. Al-Hashimi. Characterizing
Watson–Crick versus Hoogsteen Base Pairing in a DNA–Protein Complex
Using Nuclear Magnetic Resonance and Site-Specifically 13C-and
15N-Labeled DNA. Biochemistry,58, 1963-1974 (2019).
D.A. Case. Using quantum chemistry to estimate chemical shifts
in biomolecules. Biophys. Chem. 267, 106476 (2020).
O.B. Becette, G. Zong, B. Chen, K.M. Taiwo, P.Y. Zavalij, D.A.
Case and T.K. Dayie. Solution NMR Readily Reveals Structural Folds and
Interactions in Doubly Carbon-13 and Fluorine-19 Labeled RNAs. Sci. Adv.
6, eabc6572 (2020).
F. Juen, D. Glänzer, R. Plangger, V. Kugler, J. Fleischmann, E.
Stefan, D.A. Case, H. Kovacs, T.K. Dayie, C. Kreutz. Enhanced TROSY
effect in [2-19F, 2-13C] adenosine and ATP analogs facilitates NMR
spectroscopy of very large biological RNAs in solution. Angew. Chemie
136, e202316273 (2024).
A. Onufriev, D.A. Case and G.M. Ullmann. A novel view of pH titration
in biomolecules. Biochemistry 40, 3413-3419 (2001).
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.
T. Luchko, S. Gusarov, D.A. Case, J. Tuszynski and A. Kovalenko.
Three-dimensional molecular theory of solvation coupled with molecular
dynamics in Amber. J. Chem. Theory Comput. 6, 607-624 (2010)
T. Luchko, I.S. Joung and D.A. Case. Integral equation theory of
biomolecules and electrolytes. In: Innovations in Biomolecular Modeling and
Simulation, T. Schlick, ed. (London, Royal Society of Chemistry, 2012), pp.
51-86.
I.S. Joung, T. Luchko and David A. Case. Simple electrolyte
solutions: Comparison of RISM and molecular dynamics results for alkali halide
solutions. J. Chem. Phys. 138, 044103 (2013).
G.M. Giambasu, T. Luchko, D. Herschlag, D.M. York and D.A. Case.
Ion counting from explicit solvent simulations and 3D-RISM. Biophys. J.
104, 883-894 (2014). (Figure shows sodium ion
distributions around a DNA base pair.)
G.M. Giambasu, M.K. Gebala, M.T. Panteva, D.A. Case, D. Herschlag
and D.M. York. Competitive interaction of monovalent cations with DNA
predicted by 3D-RISM. Nucl. Acids Res. 43, 8405-8415 (2015).
J. Johnson, D.A. Case, T. Yamazaki, S. Gusarov, A. Kovalenko and T.
Luchko. Small Molecule Solvation Energy and Entropy from 3D-RISM. J. Phys.
Cond. Mat. 28, 344002 (2016).
G.M. Giambasu, D.A. Case, D.M. York. Predicting site-binding
modes of ions and water to nucleic acids using molecular solvation
theory. J. Am. Chem. Soc. 141, 2435-2445 (2019).
C. Nguyen, T. Yamazaki, A. Kovalenko, D.A. Case, M.K. Gilson,
T. Kurtzman, and T. Luchko. A molecular reconstruction approach to
site-based 3D-RISM and comparison to GIST hydration thermodynamic maps
in an enzyme active site. PLoS One 14, e0219473 (2019).
A.V. Onufriev and D.A. Case. Generalized Born implicit solvent
models for biomolecules. Annu. Rev. Biophys. 48, 275-296 (2019).
J.G. Gray, G.M. Giambaşu, D.A. Case and T. Luchko. Integral equation
models for solvent in macromolecular crystals. J. Chem. Phys.
156, 014801 (2022).
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).
M.C. Thielges, D.A. Case and F.E. Romesberg. Carbon-deuterium bonds as
probes of electrostatics in dihydrofolate reductase. J. Am. Chem. Soc.
130, 6597-6603 (2008).
A.A. Fuller, D. Du, F. Liu, J.E. Davoren, G. Bhabha, G. Kroon, D.A.
Case, H.J. Dyson, E.T. Powers, P. Wipf, M. Gruebele, and J.W. Kelly.
Evaluation of β-sheet folding nucleation kinetics by β-turn mimics.
Proc. Natl. Acad. Sci. USA 101, 11067-11072 (2009).
R. Chaudhuri, S. Tang, G. Zhao, H. Lu, D.A. Case and M.E. Johnson.
Comparison of SARS and NL63 papain-Like protease binding sites and binding
site dynamics: Inhibitor design implications. J. Mol. Biol. 414, 272-288
(2011). (Figure shows the electrostatic surface of
the SARS-CoV PLpro protease.)
I. Fu, D.A. Case and J. Baum. Dynamic water-mediated hydrogen bonding
in collagen model peptides. Biochemistry 54, 6029-6037 (2015).
C.L. Hoop, J. Zhu, A.M. Nunes, D.A. Case and J. Baum. Revealing
accessibility of cryptic protein binding sites within the functional collagen
fibril. Biomolecules 7, 76 (2017).
J. Zhu, C. Hoop, D.A. Case, and J. Baum. Surface Reconstruction
of the Type I Collagen Fibril Exposes Cryptic Binding Sites. Sci.
Reports 8, 16646 (2018).
C.L. Hoop, A. Kemraj, B. Wang, S. Gahlawat, M. Godesky, J. Zhu,
H.R. Warren, D.A. Case, D.I. Shreiber, and J. Baum. Molecular
underpinnings of integrin binding to vascular Ehlers-Danlos Syndrome
collagen mimetics. J. Biol. Chem. 294, 14442-14453 (2019).
P.P. Samuel, M.A. White, W.C. Ou, D.A. Case, G.N. Phillips, Jr.,
and J.S. Olson. The interplay between molten globules and heme
disassociation defines human hemoglobin disassembly. Biophys. J.
118, 1381-1400 (2020).
P.P. Samuel and D.A. Case. Atomistic simulations of heme
disassociation pathways in human methemoglobins reveal hidden
intermediates. Biochemistry 59, 4093-4107 (2020).
J.K. Williams, B. Wang, A. Sam, C.L. Hoop, D.A. Case and J.
Baum. Molecular Dynamics Analysis of a Flexible Loop Near the Binding
Interface of the Spike Protein Receptor-Binding Domain from SARS-CoV-2.
Proteins, DOI: 10.1002/prot.26208 (2021).
R.D. Palmere, D.A. Case and A.J. Nieuwkoop. Cooperative Effects of
Phosphatidyl Inositol Phosphate Protonation State on the PIP Binding
Kindlin-2 Subdomains. Biophys J. 120, 5504-5512 (2021).
E.R.P. Zuiderweg, D.A. Case and C.H. Williams, Jr. Simulating
the motion underlying the mechanism of thioredoxin reductase. ACS Omega
9, 29682-29690 (2024).
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.)
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).
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).
Y. Bomble and D.A. Case. Multiscale modeling of nucleic acids: Insights
into DNA flexibility. Biopolymers, 89, 722-731 (2008).
T.E. Cheatham, III and D.A. Case. Twenty-five years of nucleic acid
simulations. Biopolymers 99, 969-977 (2013).
M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T.
Cheatham III, B. Jayaram, F. Lankas, C. Laughton, J. Mitchel, R. Osman, M.
Orozco, D. Petkeviciute, N. Spackova, J. Sponer, K. Zakrzewska and R.
Lavery. μABC: a systematic microsecond molecular dynamics study of
tetranucleotide sequence effects in B-DNA. Nucl. Acids Res. 42,
12272-12283 (2014).
S. Ekesan, E. McCarthy, D.A. Case and D.M. York. RNA
electrostatics: How ribozymes engineer active sites to enable catalysis.
J. Phys. Chem. B 126, 5982-5990 (2022).
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.)
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).
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. 47,
3969-3977 (2008).
J.A. Fee, D.A. Case and L. Noodleman. Toward a mechanism of proton
pumping by the B-type cytochrome c oxidases: Application of density
functional theory to cytochrome ba3 from Thermus thermophilus.
J. Am. Chem. Soc. 130, 15002-15021 (2008).
V. Pelmenschikov, Y. Guo, H. Wang, S.P. Cramer and D.A. Case. Fe-H/D
stretching and bending modes in nuclear resonant vibrational, Raman and
infrared spectroscopies: Comparisons of density functional theory and
experiment. Faraday Disc. 148, 409-420 (2011).
D. Mitra, V. Pelmenschikov, Y. Guo, D.A. Case, H. Wang, W. Dong, M. Tan, T.
Ichiye, F. Jenney, Jr., M.W.W. Adams, M. Kaupp and S.P. Cramer. Dynamics of the
[4Fe-4S] Cluster in Pyrococcus furiosus Ferredoxin via Nuclear Resonance
Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy – Quantitative
Simulation by Density Functional Theory. Biochemistry 50, 5220-5235
(2011).
J.D. Kim, A. Godriguez-Ganillo, D.A. Case, V. Nanda and P.G. Falkowski.
Energetic selection of topology in ferredoxins. PLoS Comput. Biol. 8,
e1002463 (2012).
D. Mitra, S. George, J. Peters, S. Keable, V. Pelmenschikov, D.A.
Case, and S.P. Cramer. Dynamics of the [4Fe-4S] cluster in Azotobacter
vinelandii nitrogenase Fe protein in three core oxidation states via nuclear
resonance vibrational spectroscopy (NRVS). J. Am. Chem. Soc. 135,
2530-2543 (2013).
H. Chen, G.C. Dismkes and D.A. Case, Resolving Ambiguous Protonation
and Oxidation States in the Oxygen Evolving Complex of Photosystem II . J.
Phys. Chem. B 122, 8654-8664 (2018).
H. Chen, D.A. Case and G.C. Dismukes. Reconciling Structural and
Spectroscopic Fingerprints of the Oxygen Evolving Complex of Photosystem II: A
Computational Study of the S2 State. J Phys. Chem. B, 122,
11868-11882 (2018).
V. Hoeke,L. Tociu, D.A. Case, L.C. Seefeldt, S. Raugei, and
B.M. Hoffman. High resolution ENDOR spectroscopy combined with quantum
chemical calculations reveals the structure of the nitrogenase Janus
intermediate E4(4H). J. Am. Chem. Soc. 130, 11984-11996 (2019).
Updated on October 3, 2024. Comments to david.case@rutgers.edu