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501. 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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502. 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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503. Sudholt, Wibke, Baldridge, Kim K., Abramson, David, Enticott, Colin, Garic, Slavisa, (2004), "Parameter scan of an effective group difference pseudopotential using grid computing", New Generation Computing, 22, 2: pg: 137--146, 0288-3635, (DOI: 10.1007/BF03040952).
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504. Sudholt, Wibke, Baldridge, Kim K., Abramson, David, Enticott, Colin, Garic, Slavisa, (2004), "Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential": pg: 148--155, 978-3-540-22116-6 03029743, (DOI: 10.1007/978-3-540-24685-5_19).
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505. Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan A., (2004), "Finite element solution of the steady-state Smoluchowski equation for rate constant calculations.", Biophysical journal, 86, 4: pg: 2017--29, 3143622040 0006-3495, (DOI: 10.1016/S0006-3495(04)74263-0).
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506. Song, Yuhua, Zhang, Yongjie, Shen, Tongye, Bajaj, Chandrajit L., McCammon, J. Andrew, Baker, Nathan a, (2004), "Finite element solution of the steady-state Smoluchowski equation for rate constant calculations.", Biophysical journal, 86, 4: pg: 2017--29, 3143622040 0006-3495, (DOI: 10.1016/S0006-3495(04)74263-0).
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507. Sims, Peter A., Wong, Chung F., McCammon, J. Andrew, (2004), "Charge optimization of the interface between protein kinases and their ligands.", Journal of computational chemistry, 25, 11: pg: 1416--29, 0192-8651 (Print)$\backslash$r0192-8651 (Linking) (DOI: 10.1002/jcc.20067).
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508. Schames, Julie R., Henchman, Richard H., Siegel, Jay S., Sotriffer, Christoph A., Ni, Haihong, McCammon, J. Andrew, (2004), "Discovery of a novel binding trench in HIV integrase.", Journal of medicinal chemistry, 47, 8: pg: 1879--81, 0022-2623 (Print)$\backslash$n0022-2623 (Linking) (DOI: 10.1021/jm0341913).
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509. Saucerman, Jeffrey J., Healy, Sarah N., Belik, Mary E., Puglisi, Jose L., McCulloch, Andrew D., (2004), "Proarrhythmic consequences of a KCNQ1 AKAP-binding domain mutation: computational models of whole cells and heterogeneous tissue.", Circulation research, 95, 12: pg: 1216--24, 1524-4571 (Electronic)$\backslash$r0009-7330 (Link, (DOI: 10.1161/01.RES.0000150055.06226.4e).
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510. Sacerdoti, F. D., Chandra, S., Bhatia, K., (2004), "Grid systems deploment and management using Rocks", Proceedings of the \ IEEE \ International Conference on Cluster Computing: pg: 12--13
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511. Ricci, Jean-ehrland, Muoz-Pinedo, Cristina, Fitzgerald, Patrick, Bailly-Maitre, Batrice, Perkins, Guy A., Yadava, Nagendra, Scheffler, Immo E., Ellisman, Mark H., Green, Douglas R., (2004), "Disruption of mitochondrial function during apoptosis is mediated by caspase cleavage of the p75 subunit of complex I of the electron transport chain.", Cell, 117, 6: pg: 773--86, 0092-8674, (DOI: 10.1016/j.cell.2004.05.008).
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512. Perryman, Alexander L., Lin, Jung-hsin, McCammon, J. Andrew, (2004), "HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs.", Protein science : a publication of the Protein Society, 13, 4: pg: 1108--23, 0961-8368, (DOI: 10.1110/ps.03468904).
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513. Michailova, Anushka P., Belik, Mary Ellen, McCulloch, Andrew D., (2004), "Effects of magnesium on cardiac excitation-contraction coupling.", Journal of the American College of Nutrition, 23, 5: pg: 514S--517S, 0731-5724, (DOI: 10.1080/07315724.2004.10719392).
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514. Martone, Maryann E., Gupta, Amarnath, Ellisman, Mark H., (2004), "E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains.", Nature neuroscience, 7, 5: pg: 467--72, 1097-6256 (Print) 1097-6256, (DOI: 10.1038/nn1229).
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515. Hamelberg, Donald, Mongan, John, McCammon, J. Andrew, (2004), "Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.", The Journal of chemical physics, 120, 24: pg: 11919--29, 0021-9606, (DOI: 10.1063/1.1755656).
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516. Dolinsky, Todd J., Nielsen, Jens E., McCammon, J. Andrew, Baker, Nathan A., (2004), "PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.", Nucleic acids research, 32, Web Server issue: pg: W665--7, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/gkh381).
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517. Chen, Ling, McCulloch, Andrew D., May-Newman, Karen, (2004), "Nonhomogeneous deformation in the anterior leaflet of the mitral valve.", Annals of biomedical engineering, 32, 12: pg: 1599--606, 0090-6964
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518. Chen, Long, (2004), "Mesh smoothing schemes based on optimal \ Delaunay \ triangulations", 13th International Meshing Roundtable, 1: pg: 109--120
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519. Bui, Jennifer M., Tai, Kaihsu, McCammon, J. Andrew, (2004), "Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2.", Journal of the American Chemical Society, 126, 23: pg: 7198--205, 0002-7863, (DOI: 10.1021/ja0485715).
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520. Bruno, Greg, Katz, Mason J., Sacerdoti, Federico D., Papadopoulos, Philip M., (2004), "Rolls: Modifying a standard system installer to support user-customizable cluster frontend appliances", Proceedings - IEEE International Conference on Cluster Computing, ICCC: pg: 421--430, 0780386949 15525244, (DOI: 10.1109/CLUSTR.2004.1392641).
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521. Bossy-Wetzel, Ella, Talantova, Maria V., Lee, Wilson D., Schlzke, Marion N., Harrop, Anne, Mathews, Emily, Gtz, Thomas, Han, Jiahuai, Ellisman, Mark H., Perkins, Guy A., Lipton, Stuart A., (2004), "Crosstalk between nitric oxide and zinc pathways to neuronal cell death involving mitochondrial dysfunction and p38-activated K+ channels.", Neuron, 41, 3: pg: 351--65, 0896-6273 (Print) 0896-6273, (DOI: 10.1016/S0896-6273(04)00015-7).
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522. Belik, Mary E., Usyk, Taras P., McCulloch, Andrew D., (2004), "Computational Methods for Cardiac Electrophysiology", 14: pg: 129--187, (DOI: 10.1016/S1570-8659(03)12002-9).
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523. Arzberger, P., (2004), "SCIENCE AND GOVERNMENT: An International Framework to Promote Access to Data", Science, 303, 5665: pg: 1777--1778, 0036-8075, (DOI: 10.1126/science.1095958).
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524. Tchieu, Jason H., Fana, Fariba, Fink, J. Lynn, Harper, Jeffrey, Nair, T. Murlidharan, Niedner, R. Hannes, Smith, Douglas W., Steube, Kenneth, Tam, Tobey M., Veretnik, Stella, Wang, Degeng, Gribskov, Michael, (2003), "The PlantsP and PlantsT Functional Genomics Databases.", Nucleic acids research, 31, 1: pg: 342--4, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link
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525. Tai, Kaihsu, Bond, Stephen D., MacMillan, Hugh R., Baker, Nathan Andrew, Holst, Michael Jay, McCammon, J. Andrew, (2003), "Finite element simulations of acetylcholine diffusion in neuromuscular junctions.", Biophysical journal, 84, 4: pg: 2234--41, 0006-3495, (DOI: 10.1016/S0006-3495(03)75029-2).
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526. Stoffler, D., Coon, S. I., Huey, R., Olson, A. J., Sanner, M. F., (2003), "Integrating biomolecular analysis and visual programming: flexibility and interactivity in the design of bioinformatics tools": pg: 10, 0-7695-1874-5, (DOI: 10.1109/HICSS.2003.1174804).
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527. Podtelezhnikov, A. A., Gao, K., Bushman, F. D., McCammon, A., (2003), "Modelling HIV-1 Integrase Complexes Based on Their Hydrodynamic Properties", Biopolymers, 68: pg: 110--120
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528. Peltier, Steven T., Lin, Abel W., Lee, David, Mock, Stephen, Lamont, Stephan, Molina, Tomas, Wong, Mona, Dai, Lu, Martone, Maryann E., Ellisman, Mark H., (2003), "The Telescience Portal for advanced tomography applications", Journal of Parallel and Distributed Computing, 63, 5: pg: 539--550, 0743-7315 07437315, (DOI: 10.1016/S0743-7315(03)00061-3).
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529. Nielsen, Jens Erik, McCammon, J. Andrew, (2003), "On the evaluation and optimization of protein X-ray structures for pKa calculations.", Protein science : a publication of the Protein Society, 12, 2: pg: 313--26, 0961-8368, (DOI: 10.1110/ps.0229903).
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530. Li, Wilfred W., Quinn, Greg B., Alexandrov, Nickolai N., Bourne, Philip E., Shindyalov, Ilya N., (2003), "A comparative proteomics resource: proteins of Arabidopsis thaliana.", Genome biology, 4, 8: pg: R51, 1465-6914 1474-760X, (DOI: 10.1186/gb-2003-4-8-r51).
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531. Jimenez, Ralph, Salazar, Georgina, Baldridge, Kim K., Romesberg, Floyd E., (2003), "Flexibility and molecular recognition in the immune system.", Proceedings of the National Academy of Sciences of the United States of America, 100, 1: pg: 92--7, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.262411399).
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532. Fink, J. Lynn, Drewes, Scott, Patel, Hiren, Welsh, John B., Masys, Daniel R., Corbeil, Jacques, Gribskov, M., (2003), "2HAPI: a microarray data analysis system", Bioinformatics, 19, 11: pg: 1443--1445, 1367-4803, (DOI: 10.1093/bioinformatics/btg169).
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533. Bourne, Philip E., Weissig, H., (2003), "Structural bioinformatics", 1st: 3175723993
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534. Aksoylu, Burak, Bond, Stephen, Holst, Michael, (2003), "An Odyssey into Local Refinement and Multilevel Preconditioning III: Implementation and Numerical Experiments", SIAM Journal on Scientific Computing, 25, 2: pg: 478--498, 1064-8275, (DOI: 10.1137/S1064827502407676).
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535. Stoffler, Daniel, Sanner, Michel F., Morris, Garrett M., Olson, Arthur J., Goodsell, David S., (2002), "Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance.", Proteins, 48, 1: pg: 63--74, 1097-0134, (DOI: 10.1002/prot.10130).
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536. Sanner, M. F., Stoffler, Daniel, Olson, A. J., (2002), "ViPEr, a visual programming environment for Python", Proceedings of the 10th International Python conference: pg: 103--115, 1-930792-05-0
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537. Rowley, David C., Hansen, Mark S. T., Rhodes, Denise, Sotriffer, Christoph A., Ni, Haihong, McCammon, J. Andrew, Bushman, Frederic D., Fenical, William, (2002), "Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase.", Bioorganic \& medicinal chemistry, 10, 11: pg: 3619--25, 0968-0896 (Print)$\backslash$r0968-0896 (Linking) (DOI: 10.1016/S0968-0896(02)00241-9).
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538. Ponomarenko, Julia V., Bourne, Philip E., Shindyalov, Ilya N., (2002), "Building an automated classification of DNA-binding protein domains.", Bioinformatics (Oxford, England), 18 Suppl 2: pg: S192--201, 1367-4803
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539. Omens, Jeffrey H., Usyk, Taras P., Li, Zuangjie, McCulloch, Andrew D., (2002), "Muscle LIM protein deficiency leads to alterations in passive ventricular mechanics.", American journal of physiology. Heart and circulatory physiology, 282, 2: pg: H680--7, 0363-6135 (Print)$\backslash$r0363-6135 (Linking) (DOI: 10.1152/ajpheart.00773.2001).
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540. Michailova, Anushka, DelPrincipe, Franco, Egger, Marcel, Niggli, Ernst, (2002), "Spatiotemporal features of Ca2+ buffering and diffusion in atrial cardiac myocytes with inhibited sarcoplasmic reticulum.", Biophysical journal, 83, 6: pg: 3134--51, 4131631873 0006-3495, (DOI: 10.1016/S0006-3495(02)75317-4).
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541. Martone, M. E., Gupta, Amarnath, Ludascher, B., Zaslavsky, I., Ellisman, M. H., (2002), "Federation of Brain Data through Knowledge-guided Mediation", Neuroscience databases: A practical guide: Boston, Kluwer Academic Publishers: pg: 275--292
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542. Lin, Jung-Hsin, Perryman, Alexander L., Schames, Julie R., McCammon, J. Andrew, (2002), "Computational drug design accommodating receptor flexibility: the relaxed complex scheme.", Journal of the American Chemical Society, 124, 20: pg: 5632--3, 0002-7863 (Print) 0002-7863, (DOI: 10.1021/ja0260162).
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543. Lin, Jung-Hsin, Baker, Nathan A., McCammon, J. Andrew, (2002), "Bridging implicit and explicit solvent approaches for membrane electrostatics.", Biophysical journal, 83, 3: pg: 1374--9, 0006-3495, (DOI: 10.1016/S0006-3495(02)73908-8).
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544. Li, W. W., (2002), "CKAAPs DB: a Conserved Key Amino Acid Positions DataBase", Nucleic Acids Research, 30, 1: pg: 409--411, 0076-6879 (Print)$\backslash$r0076-6879 (Linking) (DOI: 10.1093/nar/30.1.409).
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545. Kuller, Anne, Fleri, Ward, Bluhm, Wolfgang F., Smith, Janet L., Westbrook, John, Bourne, Philip E., (2002), "A biologist's guide to synchrotron facilities: the BioSync web resource.", Trends in biochemical sciences, 27, 4: pg: 213--5, 0968-0004, (DOI: 10.1016/S0968-0004(02)02056-X).
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546. Henchman, Richard H., Tai, Kaihsu, Shen, Tongye, McCammon, J. Andrew, (2002), "Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation.", Biophysical journal, 82, 5: pg: 2671--82, 0006-3495, (DOI: 10.1016/S0006-3495(02)75609-9).
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547. Henchman, Richard H., McCammon, J. Andrew, (2002), "Structural and dynamic properties of water around acetylcholinesterase.", Protein science : a publication of the Protein Society, 11, 9: pg: 2080--90, 0961-8368 (Linking) 0961-8368, (DOI: 10.1110/ps.0214002).
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548. Fernndez, Jos-Jess, Lawrence, Albert F., Roca, Javier, Garcı́a, Inmaculada, Ellisman, Mark H., Carazo, Jos-Marı́a, (2002), "High-performance electron tomography of complex biological specimens", Journal of Structural Biology, 138, 1-2: pg: 6--20, 10478477, (DOI: 10.1016/S1047-8477(02)00017-5).
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549. Chien, Samson, Reiter, Lawrence T., Bier, Ethan, Gribskov, Michael, (2002), "Homophila: human disease gene cognates in Drosophila.", Nucleic acids research, 30, 1: pg: 149--51, 1362-4962 (Electronic)$\backslash$n0305-1048 (Link, (DOI: 10.1093/nar/30.1.149).
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550. Baldridge, K. K., Greenberg, J. P., Elbert, S. T., Mock, S., Papadopoulos, P., (2002), "QMView and GAMESS: Integration into the World Wide Computational Grid", July 2016: pg: 64--64, 0-7695-1524-X, (DOI: 10.1109/SC.2002.10014).
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