More recent publications (from the third millennium)

Google Scholar Profile

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.)

Techniques and miscellaneous

  • 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).

  • 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).

  • J. Liu, W.H. Miller, F. Paesani, W. Zhang, and D.A. Case. Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum. J. Chem. Phys. 131, 164509 (2009).

  • D.S. Cerutti and D.A. Case. Multi-level Ewald: A scalable variant of traditional Ewald mesh methods. J. Chem. Theory Comput. 6, 443-459 (2010).

  • 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).

  • 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).

    Structure and dynamic analysis using X-ray and cryo-EM data

  • 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).

    Structure and dynamic analysis using NMR data -- methods

  • D.A. Case. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35, 325-331 (2002).

  • 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 112, 6013-6024 (2008).

  • 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).

  • I. Bertini, D.A. Case, L. Ferella, A. Giachetti and A. Rosato. A grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics, 27, 2384-2390 (2011).

  • 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).

  • A. Gutmanas, P.D. Adams, B. Bardiaux, H.M. Berman, D.A. Case, R.H. Fogh, P. Güntert, P.M.S. Hendrickx, T. Herrmann, G.J. Kleywegt, N. Kobayashi, O. Lange, J.L. Markley, G.T. Montelione, M. Nilges, T.J. Ragan, C.D. Schwieters, R. Tejero, E. Ulrich, S. Velankar, W.F. Vranken, J. Wedell, J. Westbrook, D.S. Wishart, and G.W. Vuister. NMR exchange format: a community-driven unified representation of NMR restraints data. Nature Struct. Mol. Biol. 22, 433-434 (2015).

  • 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).

    Structure refinement using NMR data -- structures

  • 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).

  • 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).

  • 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).

  • I. Fu, D.A. Case and J. Baum. Dynamic water-mediated hydrogen bonding in collagen model peptides. Biochemistry 54, 6029-6037 (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).

    Analysis of chemical shifts and coupling constants in proteins and nucleic acids

  • 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, 13Cα, 13Cβ 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, 13Cα, 13Cβ 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)

  • 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).

  • 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. 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. (in press).

  • 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 (In press).

    Electrostatic interactions in biomolecules

  • A. Onufriev, D.A. Case and G.M. Ullmann. A novel view of pH titration in biomolecules. Biochemistry 40, 3413-3419 (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).

  • 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).

  • 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).

  • 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 and D.A. Case. Implicit solvent models and electrostatics in molecular recognition. In: Methods and Principles in Medicinal Chemistry, H. Gohlke, ed. (Weinheim, Germany: Wiley-VCH, 2012), pp. 171-189.

  • 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).

    Dynamics of peptides and proteins

  • 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)

  • 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).

  • 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).

    DNA/RNA Secondary and Tertiary Structure

  • 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).

  • 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.)

  • 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).

  • 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).

  • 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).

  • Y. Bomble and D.A. Case. Multiscale modeling of nucleic acids: Insights into DNA flexibility. Biopolymers, 89, 722-731 (2008).

  • R. Lavery, K. Zakrzewska, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham, III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, N. Spackova and J. Sponer. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res. 38, 299-313 (2010).

  • T. Gaillard and D.A. Case. Evaluation of DNA force fields in implicit solvation. J. Chem. Theory Comput. 7, 3181-3198 (2011)

  • 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).

    Active sites of iron-sulfur (and related) proteins

  • 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. Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase. J. Am. Chem. Soc. 124, 4546-4547 (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.)

  • 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. 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).

  • L. Noodleman and D.A. Case. Broken symmetry states of iron-sulfur clusters. In Encyclopedia of Inorganic Chemistry, Second Edition, R.H. Crabtree, ed. (New York, Wiley & Sons, 2009)

  • 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).

    Updated on July 12, 2018. Comments to