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401. Amaro, Rommie E., Swift, Robert V., McCammon, J. Andrew, (2007), "Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei.", PLoS neglected tropical diseases, 1, 2: pg: e68, 1935-2735, (DOI: 10.1371/journal.pntd.0000068).
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402. Zhao, Yong, Sanner, Michel F., (2007), "FLIPDock: docking flexible ligands into flexible receptors.", Proteins, 68, 3: pg: 726--37, 0887-3585 1097-0134, (DOI: 10.1002/prot.21423).
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403. Zheng, Cindy, Katz, Mason J., Papadopoulos, Phil M., Abramson, David, Ayyub, Shahaan, Enticott, Colin, Garic, Slavisa, Goscinski, Wojtek, Arzberger, Peter, Lee, Bu Sung, Phatanapherom, Sugree, Sriprayoonsakul, Somsak, Uthayopas, Putchong, Tanaka, Yoshio, Tanimur, Yusuke, (2007), "Lessons learned through driving science applications in the PRAGMA grid", International Journal of Web and Grid Services, 3, 3: pg: 287, 1741-1106, (DOI: 10.1504/IJWGS.2007.014958).
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404. Zhang, Deqiang, Gullingsrud, Justin, McCammon, J. Andrew, (2006), "Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain.", Journal of the American Chemical Society, 128, 9: pg: 3019--26, 8585348585 0002-7863, (DOI: 10.1021/ja057292u).
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405. Yerushalmi, Roie, Brandis, Alexander, Rosenbach-Belkin, Varda, Baldridge, Kim K., Scherz, Avigdor, (2006), "Modulation of fragmental charge transfer via hydrogen bonds. Direct measurement of electronic contributions.", The journal of physical chemistry. A, 110, 2: pg: 412--21, 1089-5639, (DOI: 10.1021/jp052809+).
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406. Wilmarth, P. A., Tanner, S., Dasari, S., Nagalla, S. R., Riviere, M. A., Bafna, V., Pevzner, P. A., David, L. L., (2006), "Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?", Journal of proteome research, 5, 10: pg: 2554--66, 1535-3893, (DOI: 10.1021/pr050473a).
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407. Wagoner, Jason A., Baker, Nathan Andrew, (2006), "Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms.", Proceedings of the National Academy of Sciences of the United States of America, 103, 22: pg: 8331--6, 0027-8424, (DOI: 10.1073/pnas.0600118103).
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408. Vigil, Dominico, Lin, Jung-Hsin, Sotriffer, Christoph A., Pennypacker, Juniper K., McCammon, J. Andrew, Taylor, Susan S., (2006), "A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP.", Protein science : a publication of the Protein Society, 15, 1: pg: 113--21, 0961-8368 (Print)$\backslash$n0961-8368 (Linking) (DOI: 10.1110/ps.051723606).
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409. Ung, Man-Un, Lu, Benzhuo, McCammon, J. A., (2006), "E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor.", Biopolymers, 81, 6: pg: 428--39, 1002100992 0006-3525, (DOI: 10.1002/bip.20434).
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410. Saucerman, J. J., McCulloch, A. D., (2006), "Cardiac beta-Adrenergic Signaling: From Subcellular Microdomains to Heart Failure", Annals of the New York Academy of Sciences, 1080, 1: pg: 348--361, 1573316512 0077-8923, (DOI: 10.1196/annals.1380.026).
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411. Saucerman, Jeffrey J., Zhang, Jin, Martin, Jody C., Peng, Lili X., Stenbit, Antine E., Tsien, Roger Y., McCulloch, Andrew D., (2006), "Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes.", Proceedings of the National Academy of Sciences of the United States of America, 103, 34: pg: 12923--8, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.0600137103).
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412. Perryman, Alexander L., Lin, Jung-Hsin, McCammon, J. Andrew, (2006), "Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.", Biopolymers, 82, 3: pg: 272--84, 1918-7033 0006-3525, (DOI: 10.1002/bip.20497).
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413. Onuchic, Jos N., Kobayashi, Chigusa, Miyashita, Osamu, Jennings, Patricia, Baldridge, Kim K., (2006), "Exploring biomolecular machines: energy landscape control of biological reactions.", Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361, 1472: pg: 1439--43, 0962-8436 (Print)$\backslash$r0962-8436 (Linking) (DOI: 10.1098/rstb.2006.1876).
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414. O'Rourke, Sean, Chechik, Gal, Friedman, Robin, Eskin, Eleazar, (2006), "Discrete profile comparison using information bottleneck.", BMC bioinformatics, 7 Suppl 1, Suppl 1: pg: S8, 1471-2105, (DOI: 10.1186/1471-2105-7-S1-S8).
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415. McCulloch, Andrew D., Omens, Jeffrey H., (2006), "Myocyte shearing, myocardial sheets, and microtubules.", Circulation research, 98, 1: pg: 1--3, 0000200395 1524-4571, (DOI: 10.1161/01.RES.0000200395.82480.8d).
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416. Marshall, Trevor G., Lee, Robert E., Marshall, Frances E., (2006), "Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b.", Theoretical biology \& medical modelling, 3, 1: pg: 1, 1742-4682 (Electronic)$\backslash$n1742-4682 (Link, (DOI: 10.1186/1742-4682-3-1).
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417. Marchini, Jonathan, Cutler, David, Patterson, Nick, Stephens, Matthew, Eskin, Eleazar, Halperin, Eran, Lin, Shin, Qin, Zhaohui S., Munro, Heather M., Abecasis, Goncalo R., Donnelly, Peter and, (2006), "A comparison of phasing algorithms for trios and unrelated individuals.", American journal of human genetics, 78, 3: pg: 437--50, 0002-9297 (Print) 0002-9297, (DOI: 10.1086/500808).
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418. Lorenzen-Schmidt, Ilka, Schmid-Schnbein, Geert W., Giles, Wayne R., McCulloch, Andrew D., Chien, Shu, Omens, Jeffrey H., (2006), "Chronotropic Response of Cultured Neonatal Rat Ventricular Myocytes to Short-Term Fluid Shear", Cell Biochemistry and Biophysics, 46, 2: pg: 113--122, 0000249408 1085-9195, (DOI: 10.1385/CBB:46:2:113).
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419. Li, Wilfred W., Baker, Nathan, Baldridge, Kim, McCammon, J. Andrew, Holst, Michael, McCulloch, Andrew D., Michailova, Anushka, Papadopoulos, Phil, Olson, Art, Sanner, Michel, Arzberger, Peter W., (2006), "National Biomedical Computation Resource (NBCR): Developing End-to-End$\backslash$nCyberinfrastructure for Multiscale Modeling in Biomedical Research", 2, 3: pg: 6--17
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420. Li, W. W., Krishnan, S., Mueller, K., Ichikawa, K., Date, S., Dallakyan, S., Sanner, M., Misleh, C., and, Tatebe, O., Arzberger, P. W., (2006), "Building cyberinfrastructure for bioinformatics using service oriented architecture": pg: 8 --39, 0-7695-2585-7, (DOI: 10.1109/CCGRID.2006.1630932).
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421. Lathers, A., and Kulungowski, A., Lin, A. W., Mehta, Gaurang, Peltier, S. T., Deelman, E., Ellisman, M. H., (2006), "Enabling Parallel Scientific Applications with Workflow Tools": pg: 55--60, 1-4244-0420-7, (DOI: 10.1109/CLADE.2006.1652055).
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422. Krishnan, Sriram, Stearn, Brent, Bhatia, Karan, Baldridge, Kim, Li, Wilfred, Arzberger, Peter, (2006), "Opal: SimpleWeb Services Wrappers for Scientific Applications", 18, 22: pg: 823--832, 0-7695-2669-1, (DOI: 10.1109/ICWS.2006.96).
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423. Konecny, Robert, Trylska, Joanna, Tama, Florence, Zhang, Deqiang, Baker, Nathan A., Brooks, Charles L., McCammon, J. A., (2006), "Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.", Biopolymers, 82, 2: pg: 106--20, 6176321972 0006-3525, (DOI: 10.1002/bip.20409).
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424. Kerckhoffs, R. C. P., Healy, S. N., Usyk, T. P., McCulloch, A. D., (2006), "Computational Methods for Cardiac Electromechanics", Proceedings of the IEEE, 94, 4: pg: 769--783, 0018-9219, (DOI: 10.1109/JPROC.2006.871772).
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425. Jones, Neil C., Pevzner, Pavel A., (2006), "Comparative genomics reveals unusually long motifs in mammalian genomes.", Bioinformatics (Oxford, England), 22, 14: pg: e236--42, 1367-4803 1367-4811, (DOI: 10.1093/bioinformatics/btl265).
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426. Jiang, Zhengfan, Georgel, Philippe, Li, Chenglong, Choe, Jungwoo, Crozat, Karine, Rutschmann, Sophie, Du, Xin, Bigby, Tim, Mudd, Suzanne, Sovath, Sosathya, Wilson, Ian a, Olson, Arthur, Beutler, Bruce, (2006), "Details of Toll-like receptor:adapter interaction revealed by germ-line mutagenesis.", Proceedings of the National Academy of Sciences of the United States of America, 103, 29: pg: 10961--6, 0027-8424 (Print)$\backslash$n1091-6490 (Electroni, (DOI: 10.1073/pnas.0603804103).
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427. Jain, Tushar, Cerutti, David S., McCammon, J. Andrew, (2006), "Configurational-bias sampling technique for predicting side-chain conformations in proteins.", Protein science : a publication of the Protein Society, 15, 9: pg: 2029--39, 1002100992 0961-8368, (DOI: 10.1110/ps.062165906).
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428. Ivanov, Ivaylo, Chapados, Brian R., McCammon, J. Andrew, Tainer, John A., (2006), "Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.", Nucleic acids research, 34, 20: pg: 6023--33, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/gkl744).
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429. Hunter, P. J., Li, W. W., McCulloch, A. D., Noble, Denis, (2006), "Multiscale modeling: physiome project standards, tools, and databases", Computer, 39, 11: pg: 48--54, 0018-9162, (DOI: 10.1109/MC.2006.392).
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430. Hamacher, Kay, Trylska, Joanna, McCammon, J. Andrew, (2006), "Dependency map of proteins in the small ribosomal subunit.", PLoS computational biology, 2, 2: pg: e10, 1553-7358 (Electronic) 1553-7358, (DOI: 10.1371/journal.pcbi.0020010).
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431. Gullingsrud, Justin, Kim, Choel, Taylor, Susan S., McCammon, J. Andrew, (2006), "Dynamic binding of PKA regulatory subunit RI alpha.", Structure (London, England : 1993), 14, 1: pg: 141--9, 0969-2126 (Print) 0969-2126 (Linking) 0969-2126, (DOI: 10.1016/j.str.2005.09.019).
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432. Grant, Barry J., Rodrigues, Ana P. C., ElSawy, Karim M., McCammon, J. Andrew, Caves, Leo S. D., (2006), "Bio3d: an R package for the comparative analysis of protein structures.", Bioinformatics (Oxford, England), 22, 21: pg: 2695--6, 1367-4803 1367-4811, (DOI: 10.1093/bioinformatics/btl461).
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433. Giorgione, Jennifer R., Lin, Jung-Hsin, McCammon, J. Andrew, Newton, Alexandra C., (2006), "Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment.", The Journal of biological chemistry, 281, 3: pg: 1660--9, 8585348585 0021-9258, (DOI: 10.1074/jbc.M510251200).
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434. Flaim, Sarah N., Giles, Wayne R., McCulloch, Andrew D., (2006), "Contributions of sustained INa and IKv43 to transmural heterogeneity of early repolarization and arrhythmogenesis in canine left ventricular myocytes.", American journal of physiology. Heart and circulatory physiology, 291, 6: pg: H2617--29, 0363-6135 (Print)$\backslash$r0363-6135 (Linking) (DOI: 10.1152/ajpheart.00350.2006).
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435. Eubanks, Lisa M., Rogers, Claude J., Beuscher, Albert E., Koob, George F., Olson, Arthur J., Dickerson, Tobin J., Janda, Kim D., (2006), "A molecular link between the active component of marijuana and Alzheimer's disease pathology.", Molecular pharmaceutics, 3, 6: pg: 773--7, 1543-8384, (DOI: 10.1021/mp060066m).
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436. Eskin, Eleazar, Sharan, Roded, Halperin, Eran, (2006), "A note on phasing long genomic regions using local haplotype predictions.", Journal of bioinformatics and computational biology, 4, 3: pg: 639--47, 0219-7200 (Print)$\backslash$r0219-7200 (Linking)
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437. Dzubiella, J., Swanson, J. M. J., McCammon, J. A., (2006), "Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models.", Physical review letters, 96, 8: pg: 087802, 0031-9007, (DOI: 10.1103/PhysRevLett.96.087802).
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438. Dzubiella, J., Swanson, J. M. J., McCammon, J. A., (2006), "Coupling nonpolar and polar solvation free energies in implicit solvent models.", The Journal of chemical physics, 124, 8: pg: 084905, 0021-9606, (DOI: 10.1063/1.2171192).
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439. de Oliveira, Csar Augusto F., Hamelberg, Donald, McCammon, J. Andrew, (2006), "On the application of accelerated molecular dynamics to liquid water simulations.", The journal of physical chemistry. B, 110, 45: pg: 22695--701, 1520-6106, (DOI: 10.1021/jp062845o).
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440. Costandi, Peter N., Frank, Lawrence R., McCulloch, Andrew D., Omens, Jeffrey H., (2006), "Role of diastolic properties in the transition to failure in a mouse model of the cardiac dilatation.", American journal of physiology. Heart and circulatory physiology, 291, 6: pg: H2971--9, 0363-6135, (DOI: 10.1152/ajpheart.00571.2006).
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441. Chang, Chia-En, Shen, Tongye, Trylska, Joanna, Tozzini, Valentina, McCammon, J. Andrew, (2006), "Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.", Biophysical journal, 90, 11: pg: 3880--5, 0006-3495, (DOI: 10.1529/biophysj.105.074575).
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442. Chaisson, M. J., Raphael, B. J., Pevzner, P. a, (2006), "Microinversions in mammalian evolution.", Proceedings of the National Academy of Sciences of the United States of America, 103, 52: pg: 19824--9, 0027-8424, (DOI: 10.1073/pnas.0603984103).
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443. Cerutti, David S., Jain, Tushar, McCammon, J. Andrew, (2006), "CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.", Protein science : a publication of the Protein Society, 15, 7: pg: 1579--96, 0961-8368, (DOI: 10.1110/ps.051985106).
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444. Bui, Jennifer M., Radic, Zoran, Taylor, Palmer, McCammon, J. Andrew, (2006), "Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase.", Biophysical journal, 90, 9: pg: 3280--7, 0006-3495, (DOI: 10.1529/biophysj.105.075564).
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445. Bui, Jennifer M., McCammon, J. Andrew, (2006), "Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism.", Proceedings of the National Academy of Sciences of the United States of America, 103, 42: pg: 15451--6, 0027-8424 (Print) 0027-8424, (DOI: 10.1073/pnas.0605355103).
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446. Broderick, Kate E., Feala, Jake, McCulloch, Andrew, Paternostro, Giovanni, Sharma, Vijay S., Pilz, Renate B., Boss, Gerry R., (2006), "The nitric oxide scavenger cobinamide profoundly improves survival in a Drosophila melanogaster model of bacterial sepsis.", FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 20, 11: pg: 1865--73, 1530-6860 (Electronic)$\backslash$r0892-6638 (Link, (DOI: 10.1096/fj.06-5780com).
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447. Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., (2006), "The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction.", Genome research, 16, 3: pg: 311--3, 1088-9051, (DOI: 10.1101/gr.4631806).
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448. Bhatia, Karan, Catarion, Daniel, Stearn, Brent, (2006), "Extending Grid Protocols onto the Desktop using the Mozilla Framework":
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449. Baitaluk, Michael, Sedova, Mayya, Ray, Animesh, Gupta, Amarnath, (2006), "BiologicalNetworks: visualization and analysis tool for systems biology.", Nucleic acids research, 34, Web Server issue: pg: W466--71, 1362-4962 (Electronic) 1362-4962, (DOI: 10.1093/nar/gkl308).
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450. Baitaluk, Michael, Qian, Xufei, Godbole, Shubhada, Raval, Alpan, Ray, Animesh, Gupta, Amarnath, (2006), "PathSys: integrating molecular interaction graphs for systems biology.", BMC bioinformatics, 7: pg: 55, 1471-2105 (Electronic)$\backslash$r1471-2105 (Link, (DOI: 10.1186/1471-2105-7-55).
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