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David A. Case - Publications

Chemistry & Chemical Biology Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Theoretical chemistry of biomolecules

137 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Samuel PP, Case DA. Atomistic simulations of heme dissociation pathways in human methemoglobins reveal hidden intermediates. Biochemistry. PMID 32945658 DOI: 10.1021/Acs.Biochem.0C00607  0.64
2020 Samuel PP, White MA, Ou WC, Case DA, Phillips GN, Olson JS. The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly. Biophysical Journal. PMID 32075750 DOI: 10.1016/J.Bpj.2020.01.031  0.64
2019 Cerutti DS, Case DA. Molecular Dynamics Simulations of Macromolecular Crystals. Wiley Interdisciplinary Reviews. Computational Molecular Science. 9. PMID 31662799 DOI: 10.1002/Wcms.1402  0.44
2019 Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. 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. PMID 31291328 DOI: 10.1371/Journal.Pone.0219473  0.84
2019 Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically C- and N-Labeled DNA. Biochemistry. PMID 30950607 DOI: 10.1021/Acs.Biochem.9B00027  0.4
2019 Giambasu GM, Case DA, York DM. Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory. Journal of the American Chemical Society. PMID 30632365 DOI: 10.1021/Jacs.8B11474  1
2018 Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg AE, Case DA, Walker RC, York DM. GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. Journal of Chemical Information and Modeling. PMID 30199633 DOI: 10.1021/Acs.Jcim.8B00462  1
2018 Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. Journal of Biomolecular Nmr. PMID 29675775 DOI: 10.1007/S10858-018-0177-2  0.4
2017 Cerutti DS, Debiec KT, Case DA, Chong LT. Links between the charge model and bonded parameter force constants in biomolecular force fields. The Journal of Chemical Physics. 147: 161730. PMID 29096508 DOI: 10.1063/1.4985866  0.44
2016 Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallographica. Section D, Structural Biology. 72: 1062-72. PMID 27599738 DOI: 10.1107/S2059798316012225  1
2016 Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/Acs.Jpcb.6B06414  1
2016 Hu Y, Sherborne B, Lee TS, Case DA, York DM, Guo Z. The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. Journal of Computer-Aided Molecular Design. PMID 27480697 DOI: 10.1007/S10822-016-9920-5  1
2016 Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. Journal of Chemical Theory and Computation. PMID 27399642 DOI: 10.1021/Acs.Jctc.6B00567  0.44
2016 Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T. Small molecule hydration energy and entropy from 3D-RISM. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 344002. PMID 27367817 DOI: 10.1088/0953-8984/28/34/344002  0.84
2016 Nguyen HT, Pabit SA, Pollack L, Case DA. Extracting water and ion distributions from solution x-ray scattering experiments. The Journal of Chemical Physics. 144: 214105. PMID 27276943 DOI: 10.1063/1.4953037  1
2016 Hsu CH, Park S, Mortenson DE, Foley BL, Wang X, Woods RJ, Case DA, Powers ET, Wong CH, Dyson HJ, Kelly JW. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. Journal of the American Chemical Society. PMID 27249581 DOI: 10.1021/Jacs.6B02879  1
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  0.32
2015 Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. Journal of the American Chemical Society. PMID 26306428 DOI: 10.1021/Jacs.5B07229  1
2015 Giambaşu GM, Gebala MK, Panteva MT, Luchko T, Case DA, York DM. Competitive interaction of monovalent cations with DNA from 3D-RISM. Nucleic Acids Research. 43: 8405-15. PMID 26304542 DOI: 10.1093/Nar/Gkv830  1
2015 Janowski PA, Liu C, Deckman J, Case DA. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Protein Science : a Publication of the Protein Society. PMID 26013419 DOI: 10.1002/Pro.2713  1
2015 Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. Journal of Computational Chemistry. 36: 1132-56. PMID 25914306 DOI: 10.1002/Jcc.23905  1
2015 Giamba?u GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. Rna (New York, N.Y.). 21: 963-74. PMID 25805858 DOI: 10.1261/Rna.047357.114  1
2014 Nguyen HT, Pabit SA, Meisburger SP, Pollack L, Case DA. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. The Journal of Chemical Physics. 141: 22D508. PMID 25494779 DOI: 10.1063/1.4896220  1
2014 Cerutti DS, Swope WC, Rice JE, Case DA. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. Journal of Chemical Theory and Computation. 10: 4515-4534. PMID 25328495 DOI: 10.1021/Ct500643C  1
2014 Giamba?u GM, Luchko T, Herschlag D, York DM, Case DA. Ion counting from explicit-solvent simulations and 3D-RISM. Biophysical Journal. 106: 883-94. PMID 24559991 DOI: 10.1016/J.Bpj.2014.01.021  1
2013 Breslauer KJ, Case DA, Walter NG, Woodson SA. Biopolymers celebrates 50 years of nucleic acids research. Biopolymers. 99: 909. PMID 23893377 DOI: 10.1002/Bip.22358  1
2013 Wu X, Subramaniam S, Case DA, Wu KW, Brooks BR. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. Journal of Structural Biology. 183: 429-40. PMID 23876978 DOI: 10.1016/J.Jsb.2013.07.006  1
2013 Cheatham TE, Case DA. Twenty-five years of nucleic acid simulations. Biopolymers. 99: 969-77. PMID 23784813 DOI: 10.1002/Bip.22331  1
2013 Janowski PA, Cerutti DS, Holton J, Case DA. Peptide crystal simulations reveal hidden dynamics. Journal of the American Chemical Society. 135: 7938-48. PMID 23631449 DOI: 10.1021/Ja401382Y  1
2013 Joung IS, Luchko T, Case DA. Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions. The Journal of Chemical Physics. 138: 044103. PMID 23387564 DOI: 10.1063/1.4775743  0.84
2013 Cerutti DS, Rice JE, Swope WC, Case DA. Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. The Journal of Physical Chemistry. B. 117: 2328-38. PMID 23379664 DOI: 10.1021/Jp311851R  1
2013 Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. Journal of the American Chemical Society. 135: 2530-43. PMID 23282058 DOI: 10.1021/Ja307027N  1
2013 Salomon-Ferrer R, Case DA, Walker RC. An overview of the Amber biomolecular simulation package Wiley Interdisciplinary Reviews: Computational Molecular Science. 3: 198-210. DOI: 10.1002/Wcms.1121  1
2012 Steinbrecher T, Latzer J, Case DA. Revised AMBER parameters for bioorganic phosphates. Journal of Chemical Theory and Computation. 8: 4405-4412. PMID 23264757 DOI: 10.1021/Ct300613V  1
2012 Brozell SR, Mukherjee S, Balius TE, Roe DR, Case DA, Rizzo RC. Evaluation of DOCK 6 as a pose generation and database enrichment tool. Journal of Computer-Aided Molecular Design. 26: 749-73. PMID 22569593 DOI: 10.1007/S10822-012-9565-Y  1
2011 Bertini I, Case DA, Ferella L, Giachetti A, Rosato A. A Grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics (Oxford, England). 27: 2384-90. PMID 21757462 DOI: 10.1093/Bioinformatics/Btr415  1
2010 Cerutti DS, Case DA. Multi-Level Ewald: A hybrid multigrid / Fast Fourier Transform approach to the electrostatic particle-mesh problem. Journal of Chemical Theory and Computation. 6: 443-458. PMID 22039358 DOI: 10.1021/Ct900522G  0.44
2010 Wong KF, Sonnenberg JL, Paesani F, Yamamoto T, Vaní?ek J, Zhang W, Schlegel HB, Case DA, Cheatham TE, Miller WH, Voth GA. Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology. Journal of Chemical Theory and Computation. 6: 2566-2580. PMID 21116485 DOI: 10.1021/Ct900579K  1
2010 Cerutti DS, Freddolino PL, Duke RE, Case DA. Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models. The Journal of Physical Chemistry. B. 114: 12811-24. PMID 20860388 DOI: 10.1021/Jp105813J  1
2010 Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. Journal of Chemical Theory and Computation. 6: 607-624. PMID 20440377 DOI: 10.1021/Ct900460M  1
2010 Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research. 38: 299-313. PMID 19850719 DOI: 10.1093/Nar/Gkp834  1
2010 Cerutti DS, Case DA. Multi-level ewald: A hybrid multigrid/fast fourier transform approach to the electrostatic particle-mesh problem Journal of Chemical Theory and Computation. 6: 443-458. DOI: 10.1021/ct900522g  1
2009 Liu J, Miller WH, Paesani F, Zhang W, Case DA. Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum. The Journal of Chemical Physics. 131: 164509. PMID 19894958 DOI: 10.1063/1.3254372  1
2009 Fuller AA, Du D, Liu F, Davoren JE, Bhabha G, Kroon G, Case DA, Dyson HJ, Powers ET, Wipf P, Gruebele M, Kelly JW. Evaluating beta-turn mimics as beta-sheet folding nucleators. Proceedings of the National Academy of Sciences of the United States of America. 106: 11067-72. PMID 19541614 DOI: 10.1073/Pnas.0813012106  1
2009 Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: combining techniques to model RNA-small molecule complexes. Rna (New York, N.Y.). 15: 1219-30. PMID 19369428 DOI: 10.1261/Rna.1563609  1
2009 Hou T, Xu Z, Zhang W, McLaughlin WA, Case DA, Xu Y, Wang W. Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. Molecular & Cellular Proteomics : McP. 8: 639-49. PMID 19023120 DOI: 10.1074/Mcp.M800450-Mcp200  1
2008 Thielges MC, Case DA, Romesberg FE. Carbon-deuterium bonds as probes of dihydrofolate reductase. Journal of the American Chemical Society. 130: 6597-603. PMID 18412341 DOI: 10.1021/Ja0779607  1
2008 Bomble YJ, Case DA. Multiscale modeling of nucleic acids: insights into DNA flexibility. Biopolymers. 89: 722-31. PMID 18412139 DOI: 10.1002/Bip.21000  0.68
2008 Guo Y, Wang H, Xiao Y, Vogt S, Thauer RK, Shima S, Volkers PI, Rauchfuss TB, Pelmenschikov V, Case DA, Alp EE, Sturhahn W, Yoda Y, Cramer SP. Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS). Inorganic Chemistry. 47: 3969-77. PMID 18407624 DOI: 10.1021/Ic701251J  1
2008 Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Journal of Molecular Biology. 377: 914-34. PMID 18280498 DOI: 10.1016/J.Jmb.2008.01.049  1
2008 Walker RC, Crowley MF, Case DA. The implementation of a fast and accurate QM/MM potential method in Amber. Journal of Computational Chemistry. 29: 1019-31. PMID 18072177 DOI: 10.1002/Jcc.20857  1
2008 Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J. DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Research. 36: 253-62. PMID 18025040 DOI: 10.1093/Nar/Gkm622  1
2007 Mongan J, Simmerling C, McCammon JA, Case DA, Onufriev A. Generalized Born model with a simple, robust molecular volume correction. Journal of Chemical Theory and Computation. 3: 156-169. PMID 21072141 DOI: 10.1021/ct600085e  1
2007 Lukoyanov D, Pelmenschikov V, Maeser N, Laryukhin M, Yang TC, Noodleman L, Dean DR, Case DA, Seefeldt LC, Hoffman BM. 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. Inorganic Chemistry. 46: 11437-49. PMID 18027933 DOI: 10.1021/Ic7018814  1
2007 Payne RJ, Ficht S, Tang S, Brik A, Yang YY, Case DA, Wong CH. Extended sugar-assisted glycopeptide ligations: development, scope, and applications. Journal of the American Chemical Society. 129: 13527-36. PMID 17935327 DOI: 10.1021/Ja073653P  1
2007 de M Seabra G, Walker RC, Elstner M, Case DA, Roitberg AE. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. The Journal of Physical Chemistry. A. 111: 5655-64. PMID 17521173 DOI: 10.1021/Jp070071L  1
2007 Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J. Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites. Biochemistry. 46: 3096-107. PMID 17323932 DOI: 10.1021/Bi6024269  1
2007 Grover RK, Pond SJ, Cui Q, Subramaniam P, Case DA, Millar DP, Wentworth P. O-glycoside orientation is an essential aspect of base J recognition by the kinetoplastid DNA-binding protein JBP1. Angewandte Chemie (International Ed. in English). 46: 2839-43. PMID 17295375 DOI: 10.1002/Anie.200604635  1
2006 Paesani F, Zhang W, Case DA, Cheatham TE, Voth GA. An accurate and simple quantum model for liquid water. The Journal of Chemical Physics. 125: 184507. PMID 17115765 DOI: 10.1063/1.2386157  1
2006 Xiao Y, Koutmos M, Case DA, Coucouvanis D, Wang H, Cramer SP. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields. Dalton Transactions (Cambridge, England : 2003). 2192-201. PMID 16673033 DOI: 10.1039/B513331A  1
2006 Mathews DH, Case DA. Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair. Journal of Molecular Biology. 357: 1683-93. PMID 16487974 DOI: 10.1016/J.Jmb.2006.01.054  1
2006 Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling. 25: 247-60. PMID 16458552 DOI: 10.1016/J.Jmgm.2005.12.005  1
2006 Lee BM, Xu J, Clarkson BK, Martinez-Yamout MA, Dyson HJ, Case DA, Gottesfeld JM, Wright PE. Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA. Journal of Molecular Biology. 357: 275-91. PMID 16405997 DOI: 10.1016/J.Jmb.2005.12.010  1
2006 Cui Q, Tan RKZ, Harvey SC, Case DA. Low-resolution molecular dynamics simulations of the 30S ribosomal subunit Multiscale Modeling and Simulation. 5: 1248-1263. DOI: 10.1137/05064850X  1
2006 Rizzo RC, Aynechi T, Case DA, Kuntz ID. Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial charge models and optimization of nonpolar contributions Journal of Chemical Theory and Computation. 2: 128-139. DOI: 10.1021/ct050097l  1
2006 Cheatham TE, Case DA. Using AMBER to simulate DNA and RNA Computational Studies of Rna and Dna. 45-71. DOI: 10.1007/978-1-4020-4851-3_2  1
2005 Dupradeau FY, Case DA, Yu C, Jimenez R, Romesberg FE. Differential solvation and tautomer stability of a model base pair within the minor and major grooves of DNA. Journal of the American Chemical Society. 127: 15612-7. PMID 16262427 DOI: 10.1021/Ja054607X  1
2005 Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 26: 1668-88. PMID 16200636 DOI: 10.1002/Jcc.20290  1
2005 Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P. 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. Biophysical Journal. 89: 3721-40. PMID 16169978 DOI: 10.1529/Biophysj.105.067397  1
2005 Mongan J, Case DA. Biomolecular simulations at constant pH. Current Opinion in Structural Biology. 15: 157-63. PMID 15837173 DOI: 10.1016/J.Sbi.2005.02.002  1
2004 Mongan J, Case DA, McCammon JA. Constant pH molecular dynamics in generalized Born implicit solvent. Journal of Computational Chemistry. 25: 2038-48. PMID 15481090 DOI: 10.1002/Jcc.20139  1
2004 Roberts VA, Case DA, Tsui V. Predicting interactions of winged-helix transcription factors with DNA. Proteins. 57: 172-87. PMID 15326602 DOI: 10.1002/Prot.20193  1
2004 Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, et al. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophysical Journal. 87: 3799-813. PMID 15326025 DOI: 10.1529/Biophysj.104.045252  1
2004 Zhang Q, Dwyer TJ, Tsui V, Case DA, Cho J, Dervan PB, Wemmer DE. NMR structure of a cyclic polyamide-DNA complex. Journal of the American Chemical Society. 126: 7958-66. PMID 15212545 DOI: 10.1021/Ja0373622  1
2004 Gohlke H, Kuhn LA, Case DA. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins. 56: 322-37. PMID 15211515 DOI: 10.1002/Prot.20116  1
2004 Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. Journal of Computational Chemistry. 25: 1157-74. PMID 15116359 DOI: 10.1002/Jcc.20035  1
2004 Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins. 55: 383-94. PMID 15048829 DOI: 10.1002/Prot.20033  1
2004 Roberts MF, Cui Q, Turner CJ, Case DA, Redfield AG. High-resolution field-cycling NMR studies of a DNA octamer as a probe of phosphodiester dynamics and comparison with computer simulation. Biochemistry. 43: 3637-50. PMID 15035634 DOI: 10.1021/Bi035979Q  0.44
2004 Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry. 25: 265-84. PMID 14648625 DOI: 10.1002/Jcc.10378  1
2004 Gohlke H, Case DA. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. Journal of Computational Chemistry. 25: 238-50. PMID 14648622 DOI: 10.1002/Jcc.10379  1
2003 Cui J, Crich D, Wink D, Lam M, Rheingold AL, Case DA, Fu W, Zhou Y, Rao M, Olson AJ, Johnson ME. Design and synthesis of highly constrained factor Xa inhibitors: amidine-substituted bis(benzoyl)--diazepan-2-ones and bis(benzylidene)-bis(gem-dimethyl)cycloketones. Bioorganic & Medicinal Chemistry. 11: 3379-92. PMID 12878132 DOI: 10.1016/S0968-0896(03)00332-8  1
2003 Gohlke H, Kiel C, Case DA. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. Journal of Molecular Biology. 330: 891-913. PMID 12850155 DOI: 10.1016/S0022-2836(03)00610-7  1
2003 Liu H, Qu C, Johnson JE, Case DA. Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data. Journal of Structural Biology. 142: 356-63. PMID 12781662 DOI: 10.1016/S1047-8477(03)00028-5  1
2003 Allawi HT, Kaiser MW, Onufriev AV, Ma WP, Brogaard AE, Case DA, Neri BP, Lyamichev VI. Modeling of flap endonuclease interactions with DNA substrate. Journal of Molecular Biology. 328: 537-54. PMID 12706715 DOI: 10.1016/S0022-2836(03)00351-6  1
2003 Tsui V, Macke T, Case DA. A novel method for finding tRNA genes. Rna (New York, N.Y.). 9: 507-17. PMID 12702810 DOI: 10.1261/Rna.2193703  1
2003 Gouda H, Kuntz ID, Case DA, Kollman PA. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers. 68: 16-34. PMID 12579577 DOI: 10.1002/Bip.10270  1
2003 Onufriev A, Case DA, Bashford D. Structural details, pathways, and energetics of unfolding apomyoglobin. Journal of Molecular Biology. 325: 555-67. PMID 12498802 DOI: 10.1016/S0022-2836(02)01207-X  1
2002 Onufriev A, Case DA, Bashford D. Effective Born radii in the generalized Born approximation: the importance of being perfect. Journal of Computational Chemistry. 23: 1297-304. PMID 12214312 DOI: 10.1002/Jcc.10126  1
2002 Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. Rna (New York, N.Y.). 8: 707-17. PMID 12088144 DOI: 10.1017/S1355838202028017  1
2002 Xia B, Tsui V, Case DA, Dyson HJ, Wright PE. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. Journal of Biomolecular Nmr. 22: 317-31. PMID 12018480 DOI: 10.1023/A:1014929925008  1
2002 Jimenez R, Case DA, Romesberg FE. Flexibility of an antibody binding site measured with photon echo spectroscopy Journal of Physical Chemistry B. 106: 1090-1103. DOI: 10.1021/Jp013110G  1
2001 Botuyan MV, Mer G, Yi GS, Koth CM, Case DA, Edwards AM, Chazin WJ, Arrowsmith CH. Solution structure and dynamics of yeast elongin C in complex with a von Hippel-Lindau peptide Journal of Molecular Biology. 312: 177-186. PMID 11545595 DOI: 10.1006/Jmbi.2001.4938  1
2001 Cornell W, Abseher R, Nilges M, Case DA. Continuum solvent molecular dynamics study of flexibility in interleukin-8 Journal of Molecular Graphics and Modelling. 19: 136-145. PMID 11381524 DOI: 10.1016/S1093-3263(00)00124-8  1
2001 Onufriev A, Case DA, Ullmann GM. A novel view of pH titration in biomolecules Biochemistry. 40: 3413-3419. PMID 11297406 DOI: 10.1021/bi002740q  1
2001 Tsui V, Case DA. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics Journal of Physical Chemistry B. 105: 11314-11325. DOI: 10.1021/Jp011923Z  1
2000 Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers. 56: 275-91. PMID 11754341 DOI: 10.1002/1097-0282(2000)56:4<275::Aid-Bip10024>3.0.Co;2-E  1
2000 Tsui V, Radhakrishnan I, Wright PE, Case DA. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex Journal of Molecular Biology. 302: 1101-1117. PMID 11183777 DOI: 10.1006/Jmbi.2000.4108  1
2000 Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J  1
2000 Smith JA, Bifulco G, Case DA, Boger DL, Gomez-Paloma L, Chazin WJ. The structural basis for in Situ activation of DNA alkylation by duocarmycin SA Journal of Molecular Biology. 300: 1195-1204. PMID 10903864 DOI: 10.1006/Jmbi.2000.3887  1
2000 Tsui V, Zhu L, Huang TH, Wright PE, Case DA. Assessment of zinc finger orientations by residual dipolar coupling constants Journal of Biomolecular Nmr. 16: 9-21. PMID 10718608 DOI: 10.1023/A:1008302430561  1
2000 Legge GB, Kriwacki RW, Chung J, Hommel U, Ramage P, Case DA, Dyson HJ, Wright PE. NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. Journal of Molecular Biology. 295: 1251-64. PMID 10653701 DOI: 10.1006/Jmbi.1999.3409  1
2000 Tsui V, Case DA. Molecular dynamics simulations of nucleic acids with a generalized born solvation model Journal of the American Chemical Society. 122: 2489-2498. DOI: 10.1021/Ja9939385  1
2000 Cornilescu G, Bax A, Case DA. Large variations in one-bond 13C(α)13C(β) J couplings in polypeptides correlate with backbone conformation Journal of the American Chemical Society. 122: 2168-2171. DOI: 10.1021/Ja993609C  1
2000 Case DA, Scheurer C, Bruschweiler R. Static and dynamic effects on vicinal scalar J couplings in proteins and peptides: A MD/DFT analysis Journal of the American Chemical Society. 122: 10390-10397. DOI: 10.1021/Ja001798P  1
1998 Srinivasan J, Miller J, Kollman PA, Case DA. Continuum solvent studies of the stability of RNA hairpin loops and helices. Journal of Biomolecular Structure & Dynamics. 16: 671-82. PMID 10052623 DOI: 10.1080/07391102.1998.10508279  1
1998 Cheatham TE, Srinivasan J, Case DA, Kollman PA. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. Journal of Biomolecular Structure & Dynamics. 16: 265-80. PMID 9833666 DOI: 10.1080/07391102.1998.10508245  1
1998 Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices Journal of the American Chemical Society. 120: 9401-9409. DOI: 10.1021/Ja981844+  1
1997 Wuttke DS, Foster MP, Case DA, Gottesfeld JM, Wright PE. Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. Journal of Molecular Biology. 273: 183-206. PMID 9367756 DOI: 10.1006/Jmbi.1997.1291  1
1997 Eis PS, Smith JA, Rydzewski JM, Case DA, Boger DL, Chazin WJ. High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA Journal of Molecular Biology. 272: 237-252. PMID 9299351 DOI: 10.1006/Jmbi.1997.1223  1
1997 Foster MP, Wuttke DS, Radhakrishnan I, Case DA, Gottesfeld JM, Wright PE. Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA. Nature Structural Biology. 4: 605-8. PMID 9253405 DOI: 10.1038/Nsb0897-605  1
1996 Gurbiel RJ, Doan PE, Gassner GT, Macke TJ, Case DA, Ohnishi T, Fee JA, Ballou DP, Hoffman BM. Active site structure of Rieske-type proteins: electron nuclear double resonance studies of isotopically labeled phthalate dioxygenase from Pseudomonas cepacia and Rieske protein from Rhodobacter capsulatus and molecular modeling studies of a Rieske center. Biochemistry. 35: 7834-45. PMID 8672484 DOI: 10.1021/Bi960380U  1
1995 Love JJ, Li X, Case DA, Giese K, Crosschedl R, Wright PE. Structural basis for DNA bending by the architectural transcription factor LEF-1 Nature. 376: 791-795. PMID 7651541 DOI: 10.1038/376791A0  1
1995 Potts BCM, Smith J, Akkeu M, Macke TJ, Okazaki K, Hidaka H, Case DA, Chazin WJ. The structure of calcyclin reveals a novel homodimeric fold for s100 ca2+-binding proteins Nature Structural Biology. 2: 790-796. PMID 7552751 DOI: 10.1038/Nsb0995-790  1
1995 Noodleman L, Peng CY, Case DA, Mouesca JM. Orbital interactions, electron delocalization and spin coupling in iron-sulfur clusters Coordination Chemistry Reviews. 144: 199-244. DOI: 10.1016/0010-8545(95)07011-L  1
1995 Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules Computer Physics Communications. 91: 1-41. DOI: 10.1016/0010-4655(95)00041-D  1
1994 Ösapay K, Theriault Y, Wright PE, Case DA. Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints Journal of Molecular Biology. 244: 183-197. PMID 7966330 DOI: 10.1006/Jmbi.1994.1718  1
1994 Case DA, Dyson HJ, Wright PE. Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins Methods in Enzymology. 239: 392-416. PMID 7830592 DOI: 10.1016/S0076-6879(94)39015-0  1
1992 Kavanaugh JS, Rogers PH, Case DA, Arnone A. High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site. Biochemistry. 31: 4111-21. PMID 1567857 DOI: 10.1021/Bi00131A030  1
1991 Moore JM, Lepre CA, Gippert GP, Chazin WJ, Case DA, Wright PE. High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin Journal of Molecular Biology. 221: 533-555. PMID 1920431 DOI: 10.1016/0022-2836(91)80071-2  1
1990 Gippert GP, Yip PF, Wright PE, Case DA. Computational methods for determining protein structures from NMR data Biochemical Pharmacology. 40: 15-22. PMID 2196882 DOI: 10.1016/0006-2952(90)90172-H  1
1988 Moore JM, Case DA, Chazin WJ, Gippert GP, Havel TF, Powls R, Wright PE. Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus Science. 240: 314-317. PMID 3353725 DOI: 10.1126/Science.3353725  1
1986 Tilton RF, Singh UC, Weiner SJ, Connolly ML, Kuntz ID, Kollman PA, Max N, Case DA. Computational studies of the interaction of myoglobin and xenon Journal of Molecular Biology. 192: 443-456. PMID 3560222 DOI: 10.1016/0022-2836(86)90374-8  1
1986 Case DA, McCammon JA. Dynamic simulations of oxygen binding to myoglobin Annals of the New York Academy of Sciences. 482: 222-233. PMID 3471106 DOI: 10.1111/J.1749-6632.1986.Tb20953.X  1
1983 Sontum SF, Case DA, Karplus M. Xα multiple scattering calculations on iron(II) porphine The Journal of Chemical Physics. 79: 2881-2892. DOI: 10.1063/1.446110  1
1982 Lopez JP, Yang CY, Case DA. Insulator-conductor transition in tetracyanoplatinate complexes Chemical Physics Letters. 91: 353-357. DOI: 10.1016/0009-2614(82)83299-5  1
1980 Case DA, Cook M, Karplus M. Application ofXα multiple‐scattering theory to planar organic molecules: One‐electron properties and ionization potentials of benzene, pyridine, pyrazine, pyrrole, and imidazole The Journal of Chemical Physics. 73: 3294-3313. DOI: 10.1002/Chin.198102068  1
1979 Case DA, Karplus M. Dynamics of ligand binding to heme proteins. Journal of Molecular Biology. 132: 343-68. PMID 533895 DOI: 10.1016/0022-2836(79)90265-1  1
1979 Case DA, Huynh BH, Karplus M. Binding of oxygen and carbon monoxide to hemoglobin. An analysis of the ground and excited states Journal of the American Chemical Society. 101: 4433-4453. DOI: 10.1021/ja00510a001  1
1978 Case DA, Karplus M. Stereochemistry of carbon monoxide binding to myoglobin and hemoglobin. Journal of Molecular Biology. 123: 697-701. PMID 691060 DOI: 10.1016/0022-2836(78)90214-0  1
1978 Case DA, McClelland GM, Herschbach DR. Angular momentum polarization in molecular collisions: Classical and quantum theory for measurements using resonance fluorescence Molecular Physics. 35: 541-573. DOI: 10.1080/00268977800100391  1
1977 Huynh BH, Case DA, Karplus M. Nature of the iron-oxygen bond in oxyhemoglobin. Journal of the American Chemical Society. 99: 6103-5. PMID 893879 DOI: 10.1002/Chin.197750056  1
1977 Case DA, Karplus M. Xalpha multiple scattering calculations on copper porphine. Journal of the American Chemical Society. 99: 6182-94. PMID 197139 DOI: 10.1021/Ja00461A004  1
1977 CASE DA, KARPLUS M. ChemInform Abstract: Xα MULTIPLE SCATTERING CALCULATIONS ON COPPER PORPHINE Chemischer Informationsdienst. 8. DOI: 10.1002/Chin.197751074  1
1977 HUYNH BH, CASE DA, KARPLUS M. ChemInform Abstract: NATURE OF THE IRON-OXYGEN BOND IN OXYHEMOGLOBIN Chemischer Informationsdienst. 8: no-no. DOI: 10.1002/chin.197750056  1
1976 Case DA, Karplus M. The calculation of one-electron properties from Xα multiple scattering wavefunctions Chemical Physics Letters. 39: 33-38. DOI: 10.1016/0009-2614(76)85190-1  1
1975 Case DA, Herschbach DR. Statistical theory of angular momentum polarization in chemical reactions Molecular Physics. 30: 1537-1564. DOI: 10.1080/00268977500103061  1
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