Citations

Search Citations
Citations
101. 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).
BibTex | EndNote
102. 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).
BibTex | EndNote
103. 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).
BibTex | EndNote
104. 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).
BibTex | EndNote
105. 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).
BibTex | EndNote
106. 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).
BibTex | EndNote
107. 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).
BibTex | EndNote
108. 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).
BibTex | EndNote
109. 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).
BibTex | EndNote
110. 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).
BibTex | EndNote
111. 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).
BibTex | EndNote
112. 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).
BibTex | EndNote
113. 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).
BibTex | EndNote
114. 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).
BibTex | EndNote
115. 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).
BibTex | EndNote
116. 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).
BibTex | EndNote
117. 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).
BibTex | EndNote
118. 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).
BibTex | EndNote
119. 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).
BibTex | EndNote
120. 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).
BibTex | EndNote
121. 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).
BibTex | EndNote
122. 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).
BibTex | EndNote
123. 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).
BibTex | EndNote
124. 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).
BibTex | EndNote
125. 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).
BibTex | EndNote
126. 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).
BibTex | EndNote
127. 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).
BibTex | EndNote
128. 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).
BibTex | EndNote
129. 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).
BibTex | EndNote
130. 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).
BibTex | EndNote
131. 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).
BibTex | EndNote
132. 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).
BibTex | EndNote
133. 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).
BibTex | EndNote
134. 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).
BibTex | EndNote
135. 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).
BibTex | EndNote
136. 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).
BibTex | EndNote
137. 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).
BibTex | EndNote
138. 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).
BibTex | EndNote
139. 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).
BibTex | EndNote
140. 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).
BibTex | EndNote
141. 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).
BibTex | EndNote
142. 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).
BibTex | EndNote
143. 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).
BibTex | EndNote
144. 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).
BibTex | EndNote
145. 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).
BibTex | EndNote
146. 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).
BibTex | EndNote
147. 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).
BibTex | EndNote
148. 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).
BibTex | EndNote
149. 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).
BibTex | EndNote
150. 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).
BibTex | EndNote
Reference Type
Author Geography
Author Affiliation

Export Multiple Citations

Check the citations that you would like to have exported.

|