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451. Abramson, David, Lynch, Amanda, Takemiya, Hiroshi, Tanimura, Yusuke, Date, Susumu, Nakamura, Haruki, and, and, Amoreira, Celine, Baldridge, Kim, and, and Molina, Tomas, and Arzberger, P. W., (2006), "Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons": pg: 241--248, 0-7695-2585-7, (DOI: 10.1109/CCGRID.2006.30).
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452. Adcock, Stewart a, McCammon, J. Andrew, (2006), "Molecular dynamics: survey of methods for simulating the activity of proteins.", Chemical reviews, 106, 5: pg: 1589--615, 0009-2665, (DOI: 10.1021/cr040426m).
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453. Zhang, Xiaoyu, Bajaj, Chandrajit L., Kwon, Bongjune, Dolinsky, Todd J., Nielsen, Jens E., Baker, Nathan A., (2006), "Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity.", Multiscale modeling \& simulation : a SIAM interdisciplinary journal, 5, 4: pg: 1196--1213, 8585348585 1540-3459, (DOI: 10.1137/050647670).
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454. Zhao, Yong, Stoffler, Daniel, Sanner, Michel, (2006), "Hierarchical and multi-resolution representation of protein flexibility.", Bioinformatics (Oxford, England), 22, 22: pg: 2768--74, 1367-4811 (Electronic)$\backslash$n1367-4803 (Link, (DOI: 10.1093/bioinformatics/btl481).
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455. Zhi, Degui, Krishna, S. Sri, Cao, Haibo, Pevzner, Pavel, Godzik, Adam, (2006), "Representing and comparing protein structures as paths in three-dimensional space.", BMC bioinformatics, 7, 1: pg: 460, 1471-2105, (DOI: 10.1186/1471-2105-7-460).
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456. Zhi, Degui, Raphael, Benjamin J., Price, Alkes L., Tang, Haixu, Pevzner, Pavel A., (2006), "Identifying repeat domains in large genomes.", Genome biology, 7, 1: pg: R7, 1465-6914 (Electronic)$\backslash$r1465-6906 (Link, (DOI: 10.1186/gb-2006-7-1-r7).
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457. Zhang, Deqiang, Suen, Jason, Zhang, Yongjie, Song, Yuhua, Radic, Zoran, Taylor, Palmer, Holst, Michael J., Bajaj, Chandrajit, Baker, Nathan a, McCammon, J. Andrew, (2005), "Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods.", Biophysical journal, 88, 3: pg: 1659--65, 00063495 0006-3495, (DOI: 10.1529/biophysj.104.053850).
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458. Zhang, Deqiang, McCammon, J. Andrew, (2005), "The association of tetrameric acetylcholinesterase with ColQ tail: A block normal mode analysis", PLoS Computational Biology, 1, 6: pg: 0484--0491, 1553734X, (DOI: 10.1371/journal.pcbi.0010062).
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459. Zaitlen, Noah A., Kang, Hyun Min, Feolo, Michael L., Sherry, Stephen T., Halperin, Eran, Eskin, Eleazar, (2005), "Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP.", Genome research, 15, 11: pg: 1594--600, 1088-9051 (Print) 1088-9051, (DOI: 10.1101/gr.4297805).
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460. Weis, Sara M., Zimmerman, Scott D., Shah, Maithili, Covell, James W., Omens, Jeffrey H., Ross, John, Dalton, Nancy, Jones, Ying, Reed, Charles C., Iozzo, Renato V., McCulloch, Andrew D., (2005), "A role for decorin in the remodeling of myocardial infarction.", Matrix biology : journal of the International Society for Matrix Biology, 24, 4: pg: 313--24, 0945-053X (Print)$\backslash$r0945-053X (Linking) (DOI: 10.1016/j.matbio.2005.05.003).
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461. Trylska, Joanna, Tozzini, Valentina, McCammon, J. Andrew, (2005), "Exploring global motions and correlations in the ribosome.", Biophysical journal, 89, 3: pg: 1455--63, 0006-3495 (Print) 0006-3495, (DOI: 10.1529/biophysj.104.058495).
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462. Trylska, Joanna, McCammon, J. Andrew, Brooks, Charles L., (2005), "Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach", Journal of the American Chemical Society, 127, 31: pg: 11125--11133, 0002-7863 (Print)$\backslash$n0002-7863 (Linking) (DOI: 10.1021/ja052639e).
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463. Sosinsky, Gina E., Deerinck, Thomas J., Greco, Rocco, Buitenhuys, Casey H., Bartol, Thomas M., Ellisman, Mark H., (2005), "Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography.", Neuroinformatics, 3, 2: pg: 133--62, 1539-2791 (Print) 1539-2791, (DOI: 10.1385/NI:3:2:133).
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464. Sims, Peter A., Wong, Chung F., Vuga, Danka, McCammon, J. Andrew, Sefton, Bartholomew M., (2005), "Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems", Journal of Computational Chemistry, 26, 7: pg: 668--681, 0192-8651 (Print)$\backslash$r0192-8651 (Linking) (DOI: 10.1002/jcc.20207).
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465. Shen, Tongye, Zong, Chenghang, Hamelberg, Donald, McCammon, J. Andrew, Wolynes, Peter G., (2005), "The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain.", FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 19, 11: pg: 1389--95, 0892-6638 1530-6860, (DOI: 10.1096/fj.04-3590hyp).
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466. Sanner, Michel F., (2005), "A component-based software environment for visualizing large macromolecular assemblies.", Structure (London, England : 1993), 13, 3: pg: 447--62, 0969-2126, (DOI: 10.1016/j.str.2005.01.010).
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467. Santelli, Eugenio, Leone, Marilisa, Li, Chenlong, Fukushima, Toru, Preece, Nicholas E., Olson, Arthur J., Ely, Kathryn R., Reed, John C., Pellecchia, Maurizio, Liddington, Robert C., Matsuzawa, Shu Ichi, (2005), "Structural analysis of Siah1-Siah-interacting protein interactions and insights into the assembly of an E3 ligase multiprotein complex", Journal of Biological Chemistry, 280, 40: pg: 34278--34287, 0021-9258 (Print)$\backslash$n0021-9258 (Linking) (DOI: 10.1074/jbc.M506707200).
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468. Rodrguez, Blanca, Li, Li, Eason, James C., Efimov, Igor R., Trayanova, Natalia A., (2005), "Differences between left and right ventricular chamber geometry affect cardiac vulnerability to electric shocks.", Circulation research, 97, 2: pg: 168--75, 8585348585 1524-4571, (DOI: 10.1161/01.RES.0000174429.00987.17).
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469. Minh, David D. L., Bui, Jennifer M., Chang, Chia-en, Jain, Tushar, Swanson, Jessica M. J., McCammon, J. Andrew, (2005), "The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2", Biophysical journal, 89, 4: pg: L25--L27, 00063495, (DOI: 10.1529/biophysj.105.069336).
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470. Michailova, Anushka, Saucerman, Jeffrey, Belik, Mary Ellen, McCulloch, Andrew D., (2005), "Modeling regulation of cardiac KATP and L-type Ca2+ currents by ATP, ADP, and Mg2+.", Biophysical journal, 88, 3: pg: 2234--49, 0006-3495, (DOI: 10.1529/biophysj.104.046284).
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471. Milazzo, Anna-Clare, Leblanc, Philippe, Duttweiler, Fred, Jin, Liang, Bouwer, James C., Peltier, Steve, Ellisman, Mark, Bieser, Fred, Matis, Howard S., Wieman, Howard, Denes, Peter, Kleinfelder, Stuart, Xuong, Nguyen-Huu, (2005), "Active pixel sensor array as a detector for electron microscopy.", Ultramicroscopy, 104, 2: pg: 152--9, 0304-3991, (DOI: 10.1016/j.ultramic.2005.03.006).
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472. Lu, Benzhuo, Zhang, Deqiang, McCammon, J. Andrew, (2005), "Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method", Journal of Chemical Physics, 122, 21: pg: 1--7, 00219606, (DOI: 10.1063/1.1924448).
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473. Lu, Benzhuo, Wong, Chung F., McCammon, J. Andrew, (2005), "Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.", Protein science : a publication of the Protein Society, 14, 1: pg: 159--68, 0961-8368, (DOI: 10.1110/ps.04894605).
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474. Lorenzen-Schmidt, Ilka, Stuyvers, Bruno D., ter Keurs, Henk E. D. J., Date, Moto-o, Hoshijima, Masahiko, Chien, Kenneth R., McCulloch, Andrew D., Omens, Jeffrey H., (2005), "Young MLP deficient mice show diastolic dysfunction before the onset of dilated cardiomyopathy.", Journal of molecular and cellular cardiology, 39, 2: pg: 241--50, 0000000000000 0022-2828, (DOI: 10.1016/j.yjmcc.2005.05.006).
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475. Lorenzen-Schmidt, Ilka, McCulloch, Andrew D., Omens, Jeffrey H., (2005), "Deficiency of actinin-associated LIM protein alters regional right ventricular function and hypertrophic remodeling.", Annals of biomedical engineering, 33, 7: pg: 888--96, 0000000000000 0090-6964
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476. Law, Richard J., Henchman, Richard H., McCammon, J. Andrew, (2005), "A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor.", Proceedings of the National Academy of Sciences of the United States of America, 102, 19: pg: 6813--8, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.0407739102).
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477. Krishnan, S., Stearn, B., Bhatia, K., (2005), "Web services-based data integration for life science computations":
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478. Krishnan, Sriram, Baldridge, Kim K., Greenberg, Jerry P., Stearn, Brent, Bhatia, Karan, (2005), "An end-to-end web services-based infrastructure for biomedical applications", Proceedings - IEEE/ACM International Workshop on Grid Computing, 2005: pg: 77--84, 0780394933 15505510, (DOI: 10.1109/GRID.2005.1542727).
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479. Henchman, Richard H., Wang, Hai-Long, Sine, Steven M., Taylor, Palmer, McCammon, J. Andrew, (2005), "Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain.", Biophysical journal, 88, 4: pg: 2564--76, 0006-3495, (DOI: 10.1529/biophysj.104.053934).
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480. Healy, Sarah N., McCulloch, Andrew D., (2005), "An ionic model of stretch-activated and stretch-modulated currents in rabbit ventricular myocytes.", 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, 7 Suppl 2, SUPPL. 2: pg: 128--34, 1099-5129 (Print)$\backslash$r1099-5129 (Linking) (DOI: 10.1016/j.eupc.2005.03.019).
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481. Greenberg, Jerry P., Mock, Steve, Bhatia, Karan, Katz, Mason, Bruno, Greg, Sacerdoti, Federico, Papadopoulos, Phil, Baldridge, Kim K., (2005), "Incorporation of middleware and grid technologies to enhance usability in Computational Chemistry applications", Future Generation Computer Systems, 21, 1: pg: 3--10, 3-540-22114-X 0167739X, (DOI: 10.1016/j.future.2004.09.027).
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482. Gillet, Alexandre, Sanner, Michel, Stoffler, Daniel, Olson, Arthur, (2005), "Tangible interfaces for structural molecular biology.", Structure (London, England : 1993), 13, 3: pg: 483--91, 0969-2126, (DOI: 10.1016/j.str.2005.01.009).
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483. Gao, Fan, Bren, Nina, Burghardt, Thomas P., Hansen, Scott, Henchman, Richard H., Taylor, Palmer, McCammon, J. Andrew, Sine, Steven M., (2005), "Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence", Journal of Biological Chemistry, 280, 9: pg: 8443--8451, 0021-9258 (Print) 0021-9258 00219258, (DOI: 10.1074/jbc.M412389200).
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484. Ferrarini, Luca, Bertelli, Luca, Feala, Jacob, McCulloch, Andrew D., Paternostro, Giovanni, (2005), "A more efficient search strategy for aging genes based on connectivity.", Bioinformatics (Oxford, England), 21, 3: pg: 338--48, 1367-4803, (DOI: 10.1093/bioinformatics/bti004).
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485. Estep, Donald, Holst, Michael, Larson, Mats, (2005), "Generalized Green's Functions and the Effective Domain of Influence", SIAM Journal on Scientific Computing, 26, 4: pg: 1314--1339, 1064-8275, (DOI: 10.1137/S1064827502416319).
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486. Dzubiella, J., McCammon, J. A., (2005), "Substrate concentration dependence of the diffusion-controlled steady-state rate constant.", The Journal of chemical physics, 122, 18: pg: 184902, 0021-9606, (DOI: 10.1063/1.1887165).
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487. Dang, Alan B. C., Guccione, Julius M., Zhang, Peng, Wallace, Arthur W., Gorman, Robert C., Gorman, Joseph H., Ratcliffe, Mark B., (2005), "Effect of ventricular size and patch stiffness in surgical anterior ventricular restoration: a finite element model study.", The Annals of thoracic surgery, 79, 1: pg: 185--93, 1552-6259 (Electronic)$\backslash$r0003-4975 (Link, (DOI: 10.1016/j.athoracsur.2004.06.007).
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488. Coggan, Jay S., Bartol, Thomas M., Esquenazi, Eduardo, Stiles, Joel R., Lamont, Stephan, Martone, Maryann E., Berg, Darwin K., Ellisman, Mark H., Sejnowski, Terrence J., (2005), "Evidence for ectopic neurotransmission at a neuronal synapse.", Science (New York, N.Y.), 309, 5733: pg: 446--51, 1095-9203 (Electronic)$\backslash$r0036-8075 (Link, (DOI: 10.1126/science.1108239).
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489. Coggan, Jay S., Bartol, Thomas M., Esquenazi, Eduardo, Stiles, Joel R., Lamont, Stephan, Martone, Maryann E., Berg, Darwin K., Ellisman, Mark H., Sejnowski, Terrence J., (2005), "Evidence for ectopic neurotransmission at a neuronal synapse.", Science (New York, N.Y.), 309, 5733: pg: 446--51, 1095-9203 (Electronic)$\backslash$r0036-8075 (Link, (DOI: 10.1126/science.1108239).
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490. Chen, Li, Gupta, Amarnath, Kurul, M. Erdem, (2005), "A Semantic-aware RDF Query Algebra", Proc. 11th Intl. Conf. on Management of Data, \ COMAD \ 2005:
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491. Bhatia, Karan, Chandra, Sandeep, Mueller, Kurt, (2005), "GAMA: Grid account management architecture", Proceedings - First International Conference on e-Science and Grid Computing, e-Science 2005, 2005: pg: 413--420, 0780394631, (DOI: 10.1109/E-SCIENCE.2005.45).
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492. Ashihara, Takashi, Trayanova, Natalia A., (2005), "Cell and tissue responses to electric shocks.", 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, 7 Suppl 2, SUPPL. 2: pg: 155--65, 1099-5129 (Print) 1099-5129, (DOI: 10.1016/j.eupc.2005.03.020).
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493. and Gupta, A., Kurul, M. E., (2005), "Efficient Algorithms for Pattern Matching on Directed Acyclic Graphs", Icde: pg: 384--385, 0-7695-2285-8 1084-4627, (DOI: 10.1109/ICDE.2005.56).
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494. Akiyama, Toyokazu, Teranishi, Yuuichi, Nozaki, Kazunori, Kato, Seiichi, Shimojo, Shinji, Peltier, Steven T., Lin, Abel, Molina, Tomas, Yang, George, Lee, David, Ellisman, Mark, Naito, Sei, Koike, Atsushi, Matsumoto, Shuichi, Yoshida, Kiyokazu, Mori, Hirotaro, (2005), "Scientific Grid activities and PKI deployment in the Cybermedia Center, Osaka University.", Journal of clinical monitoring and computing, 19, 4-5: pg: 279--94, 0780390741 1387-1307, (DOI: 10.1007/s10877-005-0674-1).
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495. Zhang, Deqiang, Konecny, Robert, Baker, Nathan A., McCammon, J. Andrew, (2004), "Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach", Biopolymers, 75, 4: pg: 325--337, 8585348585 0006-3525, (DOI: 10.1002/bip.20120).
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496. Yerushalmi, Roie, Scherz, Avigdor, Baldridge, Kim K., (2004), "Direct experimental evaluation of charge scheme performance by a molecular charge-meter.", Journal of the American Chemical Society, 126, 18: pg: 5897--905, 0002-7863, (DOI: 10.1021/ja039545u).
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497. Xu, Lan, Li, Chenglong, Olson, Arthur J., Wilson, Ian A., (2004), "Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening.", The Journal of biological chemistry, 279, 48: pg: 50555--65, 0021-9258 (Print)$\backslash$r0021-9258 (Linking) (DOI: 10.1074/jbc.M406801200).
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498. Xie, F., (2004), "A simulation study of the effects of cardiac anatomy in ventricular fibrillation", Journal of Clinical Investigation, 113, 5: pg: 686--693, 0021-9738, (DOI: 10.1172/JCI200417341).
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499. Trylska, Joanna, Grochowski, Pawel, McCammon, J. Andrew, (2004), "The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease.", Protein science : a publication of the Protein Society, 13, 2: pg: 513--28, 0961-8368, (DOI: 10.1110/ps.03372304).
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500. Swanson, Jessica M. J., Henchman, Richard H., McCammon, J. Andrew, (2004), "Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.", Biophysical journal, 86, 1 Pt 1: pg: 67--74, 0006-3495, (DOI: 10.1016/S0006-3495(04)74084-9).
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