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David A. Case - Publications

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

66 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
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2013 Cheatham TE, Case DA. Twenty-five years of nucleic acid simulations. Biopolymers. 99: 969-77. PMID 23784813 DOI: 10.1002/bip.22331  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.36
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.84
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  0.96
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  0.96
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  0.96
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  0.96
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  0.56
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2005 Mongan J, Case DA. Biomolecular simulations at constant pH. Current Opinion in Structural Biology. 15: 157-63. PMID 15837173 DOI: 10.1016/  0.96
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  0.56
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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
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
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: 10.1021/ja00460a047  0.96
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
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