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101. Zhou, Shenggao, Rogers, Kathleen E., de Oliveira, Csar Augusto F., Baron, Riccardo, Cheng, Li-tien, Dzubiella, Joachim, Li, Bo, McCammon, J. Andrew, (2013), "Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit 7 uril|", Journal of chemical theory and computation, 9, 9: pg: 4195--4204, 1549-9626, (DOI: 10.1021/ct400232m).
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102. Yao, Guangming, Yu, Zeyun, (2012), "A localized meshless approach for modeling spatial-temporal calcium dynamics in ventricular myocytes.", International journal for numerical methods in biomedical engineering, 28, 2: pg: 187--204, 2040-7947, (DOI: 10.1002/cnm.1453).
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103. Wereszczynski, Jeff, McCammon, J. Andrew, (2012), "Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations.", Proceedings of the National Academy of Sciences of the United States of America, 109, 20: pg: 7759--64, 1091-6490 (Electronic)$\backslash$r0027-8424 (Link, (DOI: 10.1073/pnas.1117441109).
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104. Wereszczynski, Jeff, McCammon, J. Andrew, (2012), "Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates.", Protein science : a publication of the Protein Society, 21, 4: pg: 475--86, 1469-896X (Electronic)$\backslash$r0961-8368 (Link, (DOI: 10.1002/pro.2024).
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105. Wereszczynski, Jeff, McCammon, J. Andrew, (2012), "Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition", Quarterly Reviews of Biophysics, 45, 01: pg: 1--25, 0033-5835, (DOI: 10.1017/S0033583511000096).
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106. Wang, Yi, Schlamadinger, Diana E., Kim, Judy E., McCammon, J. Andrew, (2012), "Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers.", Biochimica et biophysica acta, 1818, 5: pg: 1402--9, 0006-3002 (Print)$\backslash$n0006-3002 (Linking) (DOI: 10.1016/j.bbamem.2012.02.017).
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107. Wang, Jun, Yu, Zeyun, (2012), "Feature-sensitive tetrahedral mesh generation with guaranteed quality", Computer-Aided Design, 44, 5: pg: 400--412, 00104485, (DOI: 10.1016/j.cad.2012.01.002).
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108. Wang, Jun, Yu, Zeyun, (2012), "Feature-Preserving Mesh Denoising via Anisotropic Surface Fitting.", Journal of computer science and technology, 27, 1: pg: 163--173, 10009000 1000-9000, (DOI: 10.1007/s11390-012-1214-3).
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109. Utsintong, Maleeruk, Rojsanga, Piyanuch, Ho, Kwok-Yiu, Talley, Todd T., Olson, Arthur J., Matsumoto, Kinzo, Vajragupta, Opa, (2012), "Virtual screening against acetylcholine binding protein.", Journal of biomolecular screening, 17, 2: pg: 204--15, 1087057111421 1552-454X, (DOI: 10.1177/1087057111421667).
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110. Tveito, Aslak, Lines, Glenn Terje, Edwards, Andrew G., Maleckar, Mary M., Michailova, Anushka, Hake, Johan, McCulloch, Andrew, (2012), "Slow Calcium-Depolarization-Calcium waves may initiate fast local depolarization waves in ventricular tissue", Progress in Biophysics and Molecular Biology, 110, 2-3: pg: 295--304, 00796107, (DOI: 10.1016/j.pbiomolbio.2012.07.005).
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111. Sinko, William, de Oliveira, Csar Augusto F., Pierce, Levi C. T., McCammon, J. Andrew, (2012), "Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.", Journal of chemical theory and computation, 8, 1: pg: 17--23, 1549-9626, (DOI: 10.1021/ct200615k).
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112. Pierce, Levi C. T., Salomon-Ferrer, Romelia and, (2012), "Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics.", Journal of chemical theory and computation, 8, 9: pg: 2997--3002, 1549-9626, (DOI: 10.1021/ct300284c).
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113. Ortiz-Snchez, Juan Manuel, Bucher, Denis, Pierce, Levi C. T., Markwick, Phineus R. L., McCammon, J. Andrew, (2012), "Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics.", Journal of chemical theory and computation, 8, 8: pg: 2752--2761, 1549-9626, (DOI: 10.1021/ct200740r).
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114. Olsen, Brett N., Schlesinger, Paul H., Ory, Daniel S., Baker, Nathan A., (2012), "Side-chain oxysterols: from cells to membranes to molecules.", Biochimica et biophysica acta, 1818, 2: pg: 330--6, 0005-2736 0006-3002, (DOI: 10.1016/j.bbamem.2011.06.014).
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115. Lindert, Steffen, McCammon, J. Andrew, (2012), "Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery.", Protein science : a publication of the Protein Society, 21, 11: pg: 1734--45, 1469-896X (Electronic)$\backslash$r0961-8368 (Link, (DOI: 10.1002/pro.2155).
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116. Lindert, Steffen, Kekenes-Huskey, Peter M., McCammon, J. Andrew, (2012), "Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C.", Biophysical journal, 103, 8: pg: 1784--9, 1542-0086, (DOI: 10.1016/j.bpj.2012.08.058).
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117. Lindert, Steffen, Kekenes-Huskey, Peter M., Huber, Gary, Pierce, Levi, McCammon, J. Andrew, (2012), "Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study.", The journal of physical chemistry. B, 116, 29: pg: 8449--59, 1520-5207, (DOI: 10.1021/jp212173f).
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118. Lindert, Steffen, Kekenes-Huskey, Peter M., Huber, Gary, Pierce, Levi, McCammon, J. Andrew, (2012), "Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study.", The journal of physical chemistry. B, 116, 29: pg: 8449--59, 1520-5207, (DOI: 10.1021/jp212173f).
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119. Lindert, Steffen, Durrant, Jacob D., McCammon, J. Andrew, (2012), "LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders.", Chemical biology \& drug design, 80, 3: pg: 358--65, 1747-0285, (DOI: 10.1111/j.1747-0285.2012.01414.x).
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120. Konecny, Robert, Baker, Nathan Andrew, McCammon, James Andrew, (2012), "iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).", Computational science \& discovery, 5, 1: pg: 015005, 1749-4699, (DOI: 10.1088/1749-4699/5/1/015005).
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121. Kerckhoffs, Roy C. P., Omens, Jeffrey H., McCulloch, Andrew D., (2012), "Mechanical discoordination increases continuously after the onset of left bundle branch block despite constant electrical dyssynchrony in a computational model of cardiac electromechanics and growth.", Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology, 14 Suppl 5, suppl 5: pg: v65--v72, 1532-2092 (Electronic)$\backslash$r1099-5129 (Link, (DOI: 10.1093/europace/eus274).
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122. Kerckhoffs, Roy C. P., Omens, Jeffrey, McCulloch, Andrew D., (2012), "A single strain-based growth law predicts concentric and eccentric cardiac growth during pressure and volume overload.", Mechanics research communications, 42: pg: 40--50, 0093-6413 (Print)$\backslash$r0093-6413 (Linking) (DOI: 10.1016/j.mechrescom.2011.11.004).
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123. Kekenes-Huskey, Peter Michael, Lindert, Steffen, McCammon, James Andrew, (2012), "Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study.", PLoS computational biology, 8, 11: pg: e1002777, 1553-7358, (DOI: 10.1371/journal.pcbi.1002777).
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124. Kerckhoffs, Roy C. P., (2012), "Computational modeling of cardiac growth in the post-natal rat with a strain-based growth law.", Journal of biomechanics, 45, 5: pg: 865--71, 0021-9290 1873-2380, (DOI: 10.1016/j.jbiomech.2011.11.028).
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125. Kekenes-Huskey, P. M., Gillette, A., Hake, J., McCammon, J. Andrew, (2012), "Finite-element estimation of protein–ligand association rates with post-encounter effects: applications to calcium binding in troponin C and SERCA", Computational Science \& Discovery, 5, 1: pg: 014015, 1749-4699, (DOI: 10.1088/1749-4699/5/1/014015).
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126. Kekenes-Huskey, Peter M., Cheng, Yuhui, Hake, Johan E., Sachse, Frank B., Bridge, John H., Holst, Michael J., McCammon, J. Andrew, McCulloch, Andrew D., Michailova, Anushka P., (2012), "Modeling Effects of L-Type Ca2+ Current and Na+-Ca2+ Exchanger on Ca2+ Trigger Flux in Rabbit Myocytes with Realistic T-Tubule Geometries", Frontiers in Physiology, 3, September: pg: 351, 1664-042X (Electronic)$\backslash$r1664-042X (Link, (DOI: 10.3389/fphys.2012.00351).
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127. Hunt, Darlene L., Campbell, Patrick H., Zambon, Alexander C., Vranizan, Karen, Evans, Sylvia M., Kuo, Hai-chien, Yamaguchi, Ken D., Omens, Jeffrey H., McCulloch, Andrew D., (2012), "Early postmyocardial infarction survival in Murphy Roths Large mice is mediated by attenuated apoptosis and inflammation but depends on genetic background", Experimental Physiology, 97, 1: pg: 102--114, 09580670, (DOI: 10.1113/expphysiol.2011.060269).
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128. Hunt, Darlene L., Campbell, Patrick H., Zambon, Alexander C., Vranizan, Karen, Evans, Sylvia M., Kuo, Hai-chien, Yamaguchi, Ken D., Omens, Jeffrey H., McCulloch, Andrew D., (2012), "Early postmyocardial infarction survival in Murphy Roths Large mice is mediated by attenuated apoptosis and inflammation but depends on genetic background.", Experimental physiology, 97, 1: pg: 102--14, 1469-445X, (DOI: 10.1113/expphysiol.2011.060269).
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129. Holst, Michael, McCammon, James Andrew, Yu, Zeyun, Zhou, Youngcheng, Zhu, Yunrong, (2012), "Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation.", Communications in computational physics, 11, 1: pg: 179--214, 1815-2406, (DOI: 10.4208/cicp.081009.130611a).
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130. Holst, Michael, McCammon, J. A., Yu, Zeyun, Zhou, Y. C., Zhu, Yunrong, (2012), "Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation", Communications in Computational Physics, 11, 01: pg: 179--214, 1815-2406, (DOI: 10.4208/cicp.081009.130611a).
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131. Holst, Michael, McCammon, James Andrew, Yu, Zeyun, Zhou, Youngcheng, Zhu, Yunrong, (2012), "Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation.", Communications in computational physics, 11, 1: pg: 179--214, 1815-2406, (DOI: 10.4208/cicp.081009.130611a).
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132. Hake, Johan, Edwards, Andrew G., Yu, Zeyun, Kekenes-Huskey, Peter M., Michailova, Anushka P., McCammon, J. Andrew, Holst, Michael J., Hoshijima, Masahiko, McCulloch, Andrew D., (2012), "Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit.", The Journal of physiology, 590, 18: pg: 4403--22, 1469-7793 (Electronic)$\backslash$r0022-3751 (Link, (DOI: 10.1113/jphysiol.2012.227926).
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133. Hake, Johan, Edwards, Andrew G., Yu, Zeyun, Kekenes-Huskey, Peter M., Michailova, Anushka P., McCammon, J. Andrew, Holst, Michael J., Hoshijima, Masahiko, McCulloch, Andrew D., (2012), "Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit.", The Journal of physiology, 590, 18: pg: 4403--22, 1469-7793 (Electronic)$\backslash$r0022-3751 (Link, (DOI: 10.1113/jphysiol.2012.227926).
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134. Gao, Zhanheng, Yu, Zeyun, Holst, Michael, (2012), "Quality Tetrahedral Mesh Smoothing via Boundary-Optimized Delaunay Triangulation.", Computer aided geometric design, 29, 9: pg: 707--721, 1191001202 0167-8396, (DOI: 10.1016/j.cagd.2012.07.001).
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135. Forli, Stefano, Olson, Arthur J., (2012), "A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.", Journal of medicinal chemistry, 55, 2: pg: 623--38, 0022-2623 1520-4804, (DOI: 10.1021/jm2005145).
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136. Feala, Jacob D., Cortes, Jorge, Duxbury, Phillip M., McCulloch, Andrew D., Piermarocchi, Carlo, Paternostro, Giovanni, (2012), "Statistical properties and robustness of biological controller-target networks.", PloS one, 7, 1: pg: e29374, 9781584885399 1932-6203, (DOI: 10.1371/journal.pone.0029374).
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137. Durrant, Jacob D., McCammon, J. Andrew, (2012), "AutoClickChem: click chemistry in silico.", PLoS computational biology, 8, 3: pg: e1002397, 1553-7358, (DOI: 10.1371/journal.pcbi.1002397).
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138. Cosconati, Sandro, Marinelli, Luciana and, (2012), "Protein flexibility in virtual screening: the BACE-1 case study.", Journal of chemical information and modeling, 52, 10: pg: 2697--704, 1549-960X, (DOI: 10.1021/ci300390h).
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139. Bauler, Patricia, Huber, Gary A., McCammon, J. Andrew, (2012), "Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.", The Journal of chemical physics, 136, 16: pg: 164107, 1089-7690, (DOI: 10.1063/1.4704808).
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140. Autin, Ludovic, Johnson, Graham, Hake, Johan, Olson, Arthur, Sanner, Michel, (2012), "uPy: a ubiquitous CG Python API with biological-modeling applications.", IEEE computer graphics and applications, 32, 5: pg: 50--61, 0272-1716 VO - 32 1558-1756, (DOI: 10.1109/MCG.2012.93).
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141. and Irturk, Ali, Kastner, Ryan, McCulloch, Andrew, Omens, Jeffrey, Wright, Adam, (2012), "GPU acceleration of optical mapping algorithm for cardiac electrophysiology", 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012: pg: 1558--1561, 978-1-4577-1787-1 1557-170X, (DOI: 10.1109/EMBC.2012.6346240).
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142. Yu, Zeyun, Yao, Guangming, Hoshijima, Masahiko, Michailova, Anushka, Holst, Michael, (2011), "Multiscale modeling of calcium dynamics in ventricular myocytes with realistic transverse tubules.", IEEE transactions on bio-medical engineering, 58, 10: pg: 2947--51, 0018-9294 VO - 58 1558-2531, (DOI: 10.1109/TBME.2011.2158316).
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143. Williams, Sarah L., de Oliveira, Csar Augusto F., Vazquez, H., McCammon, J. Andrew, (2011), "From Zn to Mn: the study of novel manganese-binding groups in the search for new drugs against tuberculosis.", Chemical biology \& drug design, 77, 2: pg: 117--23, 1747-0285 (Electronic)$\backslash$r1747-0277 (Link, (DOI: 10.1111/j.1747-0285.2010.01060.x).
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144. Williams, Sarah L., Blachly, Patrick G., McCammon, J. Andrew, (2011), "Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.", Proteins, 79, 12: pg: 3381--8, 1097-0134 (Electronic)$\backslash$r0887-3585 (Link, (DOI: 10.1002/prot.23136).
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145. Wang, Yi, Markwick, Phineus R. L., de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2011), "Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics", Journal of Chemical Theory and Computation, 7, 10: pg: 3199--3207, 1549-9618, (DOI: 10.1021/ct200430c).
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146. Wang, Yi, Harrison, Christopher B., Schulten, Klaus, McCammon, J. Andrew, (2011), "Implementation of Accelerated Molecular Dynamics in NAMD.", Computational science \& discovery, 4, 1: pg: 015002, 1749-4699 (Electronic) 1749-4699, (DOI: 10.1088/1749-4699/4/1/015002).
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147. Wang, Yi, Hess, Tamara Noelle, Jones, Victoria, Zhou, Joe Zhongxiang, McNeil, Michael R. and, (2011), "Novel inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) identified by virtual screening.", Bioorganic \& medicinal chemistry letters, 21, 23: pg: 7064--7, 1464-3405, (DOI: 10.1016/j.bmcl.2011.09.094).
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148. Wang, Jun, Yu, Zeyun, (2011), "Quality Mesh Smoothing via Local Surface Fitting and Optimum Projection.", Graphical models, 73, 4: pg: 127--139, 1524-0703, (DOI: 10.1016/j.gmod.2011.01.002).
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149. Unni, Samir, Huang, Yong, Hanson, Robert M., Tobias, Malcolm, Krishnan, Sriram, Li, Wilfred W., Nielsen, Jens E., Baker, Nathan A., (2011), "Web servers and services for electrostatics calculations with APBS and PDB2PQR.", Journal of computational chemistry, 32, 7: pg: 1488--91, 1096-987X, (DOI: 10.1002/jcc.21720).
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150. Torres, Rodrigo, Swift, Robert V., Chim, Nicholas, Wheatley, Nicole, Lan, Benson, Atwood, Brian R., Pujol, Cline, Sankaran, Banu, Bliska, James B., Amaro, Rommie E., Goulding, Celia W., (2011), "Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.", PloS one, 6, 9: pg: e25084, 1932-6203 (Electronic) 1932-6203 (Linking) 1932-6, (DOI: 10.1371/journal.pone.0025084).
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