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51. Votapka, Lane W., Amaro, Rommie E., (2015), "Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.", PLoS computational biology, 11, 10: pg: e1004381, 1553-7358, (DOI: 10.1371/journal.pcbi.1004381).
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52. Vincent, Kevin P., Gonzales, Matthew J., Gillette, Andrew K., Villongco, Christopher T., Pezzuto, Simone, Omens, Jeffrey H., Holst, Michael J., McCulloch, Andrew D., (2015), "High-order finite element methods for cardiac monodomain simulations", Frontiers in Physiology, 6, Aug: pg: 1--9, 1664042X, (DOI: 10.3389/fphys.2015.00217).
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53. Takeshima, Hiroshi, Hoshijima, Masahiko, Song, Long Sheng, (2015), "Ca \textless sup \textgreater 2+ \textless /sup \textgreater microdomains organized by junctophilins", Cell Calcium, 58, 4: pg: 349--356, 15321991, (DOI: 10.1016/j.ceca.2015.01.007).
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54. Scott, William L., Denton, Ryan E., Marrs, Kathleen A., Durrant, Jacob D., Samaritoni, J. Geno, Abraham, Milata M., Brown, Stephen P., Carnahan, Jon M., Fischer, Lindsey G., Glos, Courtney E., Sempsrott, Peter J., O'Donnell, Martin J., (2015), "Distributed drug discovery: Advancing chemical education through contextualized combinatorial solid-phase organic laboratories", Journal of Chemical Education, 92, 5: pg: 819--826, 19381328, (DOI: 10.1021/ed500135n).
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55. Richards, Christopher, Albin, John S., Demir, zlem, Shaban, Nadine M., Luengas, Elizabeth M., Land, Allison M., Anderson, Brett D., Holten, John R., Anderson, John S., Harki, Daniel A., Amaro, Rommie E., Harris, Reuben S., (2015), "The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches.", Cell reports, 13, 9: pg: 1781--8, 2211-1247, (DOI: 10.1016/j.celrep.2015.10.067).
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56. Perkins, Guy A., Jackson, Dakota R., Spirou, George A., (2015), "Resolving presynaptic structure by electron tomography", Synapse, 69, 5: pg: 268--282, 0887-4476 10982396, (DOI: 10.1002/syn.21813).
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57. Muzic, Mathieu Le, Autin, Ludovic, Parulek, Julius, Viola, Ivan, (2015), "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets": (DOI: 10.2312/vcbm.20151209).
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58. Morotti, Stefano, McCulloch, Andrew D., Bers, Donald M., Edwards, Andrew G., Grandi, Eleonora, (2015), "Atrial-selective targeting of arrhythmogenic phase-3 early afterdepolarizations in human myocytes", Journal of Molecular and Cellular Cardiology: 10958584, (DOI: 10.1016/j.yjmcc.2015.07.030).
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59. Miao, Yinglong, Feher, Victoria A., McCammon, J. Andrew, (2015), "Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.", Journal of chemical theory and computation, 11, 8: pg: 3584--3595, 1549-9626, (DOI: 10.1021/acs.jctc.5b00436).
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60. Malmstrom, Robert D., Kornev, Alexandr P., Taylor, Susan S., Amaro, Rommie E., (2015), "Allostery through the computational microscope: cAMP activation of a canonical signalling domain.", Nature communications, 6, May: pg: 7588, 2041-1723, (DOI: 10.1038/ncomms8588).
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61. Lindert, Steffen, Cheng, Yuanhua, Kekenes-Huskey, Peter, Regnier, Michael, McCammon, J. Andrew, (2015), "Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations", Biophysical Journal, 108, 2: pg: 395--407, 15420086, (DOI: 10.1016/j.bpj.2014.11.3461).
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62. Komin, Niko, Moein, Mahsa, Ellisman, Mark H., Skupin, Alexander, (2015), "Multiscale Modeling Indicates That Temperature Dependent Ca2+ i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity.", Neural plasticity, 2015: pg: 683490, 1687-5443, (DOI: 10.1155/2015/683490).
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63. Kim, Meekyum Olivia, Feng, Xinxin, Feixas, Ferran, Zhu, Wei, Lindert, Steffen, Bogue, Shannon, Sinko, William and, (2015), "A molecular dynamics investigation of Mycobacterium tuberculosis prenyl synthases: Conformational flexibility and implications for computer-aided drug discovery", Chemical Biology and Drug Design, 85, 6: pg: 756--769, 17470285, (DOI: 10.1111/cbdd.12463).
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64. Kim, M. Olivia, Blachly, Patrick G., McCammon, J. Andrew, (2015), "Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.", PLoS computational biology, 11, 10: pg: e1004341, 1553-7358, (DOI: 10.1371/journal.pcbi.1004341).
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65. Kappel, Kalli, Miao, Yinglong, McCammon, J. Andrew, (2015), "Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor.", Quarterly reviews of biophysics, 48, 4: pg: 479--87, 1469-8994, (DOI: 10.1017/S0033583515000153).
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66. Jones, Cory, Liu, Ting, Cohan, Nathaniel Wood, Ellisman, Mark, Tasdizen, Tolga, (2015), "Efficient semi-automatic 3D segmentation for neuron tracing in electron microscopy images", Journal of Neuroscience Methods, 246: pg: 13--21, 1872678X, (DOI: 10.1016/j.jneumeth.2015.03.005).
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67. Gilbert, Kathleen, Farrar, Genevieve, Cowan, Brett R., Suinesiaputra, Avan, Occleshaw, Christopher, Pontre, Beau, Perry, James, Hegde, Sanjeet, Marsden, Alison, Omens, Jeff, McCulloch, Andrew, Young, Alistair A., (2015), "Creating shape templates for patient specific biventricular modeling in congenital heart disease", Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2015-Novem: pg: 679--682, 9781424492718 1557170X, (DOI: 10.1109/EMBC.2015.7318453).
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68. Feng, Xinxin, Zhu, Wei, Schurig-Briccio, Lici a, Lindert, Steffen, Shoen, Carolyn, Hitchings, Reese, Li, Jikun, Wang, Yang, Baig, Noman, Zhou, Tianhui, Kim, Boo Kyung, Crick, Dean C., Cynamon, Michael, McCammon, J. Andrew, Gennis, Robert B., Oldfield, Eric, (2015), "Antiinfectives targeting enzymes and the proton motive force.", Proceedings of the National Academy of Sciences of the United States of America, 112, 51: pg: E7073--82, 1091-6490, (DOI: 10.1073/pnas.1521988112).
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69. Durrant, Jacob D., Carlson, Kathryn E., Martin, Teresa A., Offutt, Tavina L., Mayne, Christopher G., Katzenellenbogen, John A., Amaro, Rommie E., (2015), "Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands", Journal of Chemical Information and Modeling, 55, 9: pg: 1953--1961, 1549-9596, (DOI: 10.1021/acs.jcim.5b00241).
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70. Durrant, Jacob D., Amaro, Rommie E., (2015), "Machine-learning techniques applied to antibacterial drug discovery.", Chemical biology \& drug design, 85, 1: pg: 14--21, 1747-0285 (Electronic)$\backslash$r1747-0277 (Link, (DOI: 10.1111/cbdd.12423).
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71. de Oliveira, Bernardo L., Pfeiffer, Emily R., Sundnes, Joakim, Wall, Samuel T., McCulloch, Andrew D., (2015), "Increased Cell Membrane Capacitance is the Dominant Mechanism of Stretch-Dependent Conduction Slowing in the Rabbit Heart: A Computational Study", Cellular and Molecular Bioengineering, 8, 2: pg: 237--246, 1865-5025, (DOI: 10.1007/s12195-015-0384-9).
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72. Cheng, Yuanhua, Rao, Vijay, Tu, An-Yue, Lindert, Steffen, Wang, Dan, Oxenford, Lucas, McCulloch, Andrew D., McCammon, J. Andrew, Regnier, Michael, (2015), "Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation.", The Journal of biological chemistry, 290, 46: pg: 27749--66, 1083-351X, (DOI: 10.1074/jbc.M115.683045).
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73. Boras, Britton W., Hirakis, Sophia P., Votapka, Lane W., Malmstrom, Robert D., Amaro, Rommie E., McCulloch, Andrew D., (2015), "Bridging scales through multiscale modeling: a case study on protein kinase A.", Frontiers in physiology, 6, September: pg: 250, 1664-042X, (DOI: 10.3389/fphys.2015.00250).
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74. Antonucci, Laura, Fagman, Johan B., Kim, Ju Youn, Todoric, Jelena, Gukovsky, Ilya, Mackey, Mason, Ellisman, Mark H., Karin, Michael, (2015), "Basal autophagy maintains pancreatic acinar cell homeostasis and protein synthesis and prevents ER stress.", Proceedings of the National Academy of Sciences of the United States of America, 112, 45: pg: E6166--74, 1091-6490, (DOI: 10.1073/pnas.1519384112).
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75. Sundnes, J., Wall, S., Osnes, H., Thorvaldsen, T., McCulloch, a D., (2014), "Improved discretisation and linearisation of active tension in strongly coupled cardiac electro-mechanics simulations.", Computer methods in biomechanics and biomedical engineering, 17, 6: pg: 604--15, 1476-8259, (DOI: 10.1080/10255842.2012.704368).
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76. Pfeiffer, Emily R., Tangney, Jared R., Omens, Jeffrey H., McCulloch, Andrew D., (2014), "Biomechanics of Cardiac Electromechanical Coupling and Mechanoelectric Feedback", Journal of Biomechanical Engineering, 136, 2: pg: 021007, 0148-0731, (DOI: 10.1115/1.4026221).
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77. Lyon, Robert C., Mezzano, Valeria, Wright, Adam T., Pfeiffer, Emily, Chuang, Joyce, Banares, Katherine, Castaneda, Allan, Ouyang, Kunfu, Cui, Li, Contu, Riccardo, Gu, Yusu, Evans, Sylvia M., Omens, Jeffrey H., Peterson, Kirk L., McCulloch, Andrew D., Sheikh, Farah, (2014), "Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model", Human Molecular Genetics, 23, 5: pg: 1134--1150, 1460-2083 (Electronic)$\backslash$r0964-6906 (Link, (DOI: 10.1093/hmg/ddt508).
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78. Banerjee, Indroneal, Zhang, Jianlin, Moore-Morris, Thomas, Pfeiffer, Emily, Buchholz, Kyle S., Liu, Ao, Ouyang, Kunfu, Stroud, Matthew J., Gerace, Larry, Evans, Sylvia M., McCulloch, Andrew, Chen, Ju, (2014), "Targeted Ablation of Nesprin 1 and Nesprin 2 from Murine Myocardium Results in Cardiomyopathy, Altered Nuclear Morphology and Inhibition of the Biomechanical Gene Response", PLoS Genetics, 10, 2: pg: e1004114, 1553-7404 (Electronic)$\backslash$r1553-7390 (Link, (DOI: 10.1371/journal.pgen.1004114).
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79. Wang, Nuo, Huber, Gary A., McCammon, J. Andrew, (2013), "Assessing the two-body diffusion tensor calculated by the bead models", Journal of Chemical Physics, 138, 20: pg: 1--8, 00219606, (DOI: 10.1063/1.4807590).
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80. Wan, Xiaohua, Phan, Sbastien, Lawrence, Albert, Zhang, Fa, Han, Renmin, Liu, Zhiyong, Ellisman, Mark, (2013), "Iterative Methods in Large Field Electron Microscope Tomography", SIAM Journal on Scientific Computing, 35, 5: pg: S402--S419, 1064-8275, (DOI: 10.1137/120881464).
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81. Votapka, Lane, Amaro, Rommie E., (2013), "Multistructural hot spot characterization with FTProd.", Bioinformatics (Oxford, England), 29, 3: pg: 393--4, 1367-4803 1367-4811, (DOI: 10.1093/bioinformatics/bts689).
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82. Sinko, William, Miao, Yinglong, de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2013), "Population Based Reweighting of Scaled Molecular Dynamics", The Journal of Physical Chemistry B, 117, 42: pg: 12759--12768, 1520-6106, (DOI: 10.1021/jp401587e).
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83. Rogers, Kathleen E., Ortiz-Snchez, Juan Manuel, Baron, Riccardo, Fajer, Mikolai, de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2013), "On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations.", Journal of chemical theory and computation, 9, 1: pg: 46--53, 1549-9626, (DOI: 10.1021/ct300515n).
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84. Rao, Vijay S., Lindert, Steffen, Wang, Dan D., Kekenes-Huskey, Peter, Cheng, Yuanhua, McCammon, J. Andrew, McCulloch, Andrew, Arzberger, Peter, Regnier, Michael, (2013), "Mechanisms of Altered Cardiac Myofibril Relaxation Caused by the Cardiac Troponin-I R145G Mutation", Biophysical Journal, 104, 2: pg: 311a, 00063495, (DOI: 10.1016/j.bpj.2012.11.1728).
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85. Park, Jiho, Czapla, Luke, Amaro, Rommie E., (2013), "Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding.", Journal of chemical information and modeling, 53, 8: pg: 2047--56, 1549-9596 1549-960X, (DOI: 10.1021/ci400225w).
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86. Orloff, David N., Iwasa, Janet H., Martone, Maryann E., Ellisman, Mark H., Kane, Caroline M., (2013), "The cell: An image library-CCDB: A curated repository of microscopy data", Nucleic Acids Research, 41, D1: 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/gks1257).
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87. Nichols, Sara E., Hernndez, Carlos X., Wang, Yi, McCammon, James Andrew, (2013), "Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface", Protein Science, 22, 6: pg: 745--754, 1469-896X 09618368, (DOI: 10.1002/pro.2258).
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88. Miao, Yinglong, Nichols, Sara E., Gasper, Paul M., Metzger, Vincent T., McCammon, J. Andrew, (2013), "Activation and dynamic network of the M2 muscarinic receptor.", Proceedings of the National Academy of Sciences of the United States of America, 110, 27: pg: 10982--7, 1091-6490, (DOI: 10.1073/pnas.1309755110).
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89. Lindert, Steffen, Meiler, Jens, McCammon, J. Andrew, (2013), "Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality.", Journal of chemical theory and computation, 9, 8: pg: 3843--3847, 1549-9626, (DOI: 10.1021/ct400260c).
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90. Lo, Yuan Hung, Peachey, Tom, Abramson, David, McCulloch, Andrew, Michailova, Anushka, (2013), "Sensitivity of rabbit ventricular action potential and Ca²⁺ dynamics to small variations in membrane currents and ion diffusion coefficients.", BioMed research international, 2013: pg: 565431, 2314-6141, (DOI: 10.1155/2013/565431).
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91. Lindert, Steffen, Bucher, Denis, Eastman, Peter, Pande, Vijay, McCammon, J. Andrew, (2013), "Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units", Journal of Chemical Theory and Computation, 9, 11: pg: 4684--4691, 1549-9618, (DOI: 10.1021/ct400514p).
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92. Krishnamurthy, Adarsh, Villongco, Christopher T., Chuang, Joyce, Frank, Lawrence R., Nigam, Vishal, Belezzuoli, Ernest, Stark, Paul, Krummen, David E., Narayan, Sanjiv, Omens, Jeffrey H., McCulloch, Andrew D., Kerckhoffs, Roy C. P., (2013), "Patient-specific models of cardiac biomechanics", Journal of Computational Physics, 244: pg: 4--21, 00219991, (DOI: 10.1016/j.jcp.2012.09.015).
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93. Kim, Meekyum Olivia, Nichols, Sara E., Wang, Yi, McCammon, J. Andrew, (2013), "Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC", Journal of Computer-Aided Molecular Design, 27, 3: pg: 235--246, 1573-4951 (Electronic)$\backslash$r0920-654X (Link, (DOI: 10.1007/s10822-013-9643-9).
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94. Kekenes-Huskey, Peter M., Liao, Tao, Gillette, Andrew K., Hake, Johan E., Zhang, Yongjie, Michailova, Anushka P., McCulloch, Andrew D., McCammon, J. Andrew, (2013), "Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice", Biophysical Journal, 105, 9: pg: 2130--2140, 00063495, (DOI: 10.1016/j.bpj.2013.09.020).
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95. Feher, Victoria A., Randall, Arlo, Baldi, Pierre, Bush, Robin M., de la Maza, Luis M., Amaro, Rommie E., (2013), "A 3-Dimensional Trimeric $\beta$-Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram-Negative Bacterial Porins", PLoS ONE, 8, 7: pg: e68934, 1932-6203, (DOI: 10.1371/journal.pone.0068934).
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96. Eun, Changsun, Kekenes-Huskey, Peter M., McCammon, J. Andrew, (2013), "Influence of neighboring reactive particles on diffusion-limited reactions", Journal of Chemical Physics, 139, 4: pg: 1--10, 1089-7690 (Electronic)$\backslash$r0021-9606 (Link, (DOI: 10.1063/1.4816522).
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97. Durrant, Jacob D., Lindert, Steffen, McCammon, J. Andrew, (2013), "AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.", Journal of molecular graphics \& modelling, 44: pg: 104--12, 1873-4243, (DOI: 10.1016/j.jmgm.2013.05.006).
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98. Durrant, Jacob D., Friedman, Aaron J., Rogers, Kathleen E., McCammon, J. Andrew, (2013), "Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening", Journal of Chemical Information and Modeling, 53, 7: pg: 1726--1735, 1549-9596, (DOI: 10.1021/ci400042y).
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99. Arrar, Mehrnoosh, de Oliveira, Cesar Augusto F., Fajer, Mikolai, Sinko, William, McCammon, J. Andrew, (2013), "w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations.", Journal of chemical theory and computation, 9, 1: pg: 18--23, 1549-9626, (DOI: 10.1021/ct300896h).
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100. Arrar, Mehrnoosh, Turnham, Rigney, Pierce, Levi, de Oliveira, Cesar Augusto F., McCammon, J. Andrew, (2013), "Structural insight into the separate roles of inositol tetraphosphate and deacetylase-activating domain in activation of histone deacetylase 3.", Protein science : a publication of the Protein Society, 22, 1: pg: 83--92, 1469-896X (Electronic)$\backslash$r0961-8368 (Link, (DOI: 10.1002/pro.2190).
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