National Biomedical Computation Resource

Publications

Award Period: III | II | I

Award Period III (5/1/2004 - )

for preprints & reprints, please visit NBCR Pre/Reprints Repository

* indicates P41 RR008605 Grant Acknowledged

1. * 0001: Amaro, R. E.; Minh, D. D.; Cheng, L. S.; Lindstrom, W. M., Jr.; Olson, A. J.; Lin, J. H.; Li, W. W.; McCammon, J. A., Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc 2007, 129, (25), 7764-5, Pubmed
2. * 0005: Amaro, R. E.; Newhouse, I.; Xu, D.; Choi, Y.; Cheng, L. S.; Ding, Z.; Luo, Z.; Goodman, W.; Lin, J.-H.; Wahab, H.; Tatebe, O.; Tanimura, Y.; Jeong, K.; Nan, K.; Wei, X.; Lee, J.; Alam, M.; McCammon, J. A.; Li, W. W.; Arzberger, P. W. In Avian Flu Grid: International Collaborative Environment for Team Science on Avian Influenza, PRAGMA 13 Workshop, Urbana-Champaign, Illinois, 2007; Urbana-Champaign, Illinois, 2007,
3. * 0001: Amaro, R. E.; Swift, R. V.; McCammon, J. A., FUNCTIONAL AND STRUCTURAL INSIGHTS REVEALED BY MOLECULAR DYNAMICS SIMULATIONS OF AN ESSENTIAL RNA EDITING LIGASE IN TRYPANOSOMA BRUCEI. PLoS Neglected Tropical Diseases 2007, In Press,
4. 0001: Babakhani, A.; Gorfe, A. A.; Gullingsrud, J.; Kim, J. E.; McCammon, J. A., Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulation. Biopolymers 2007, 85, (5-6), 490-497, Pubmed
5. 0001: Baker, N. A.; McCammon, J. A., Electrostatic Interactions. In Structural Bioinformatics, Bourne, P. E.; Gu, J., Eds. John Wiley & Sons: New York, 2007,
6. * 0001: Baron, R.; McCammon, J. A., Dynamics, Hydration, and Motional Averaging of a Loop-Gated Artificial Protein Cavity: The W191G Mutant of Cytochrome c Peroxidase in Water as Revealed by Molecular Dynamics Simulations. Biochemistry 2007, 46, (37), 10629-42, Pubmed
7. 0005: Bencheikh-Latmani, R.; Obraztsova, A.; Mackey, M. R.; Ellisman, M. H.; Tebo, B. M., Toxicity of Cr(lll) to Shewanella sp. strain MR-4 during Cr(VI) reduction. Environ Sci Technol 2007, 41, (1), 214-20, Pubmed
8. 0005: Bielas, S. L.; Serneo, F. F.; Chechlacz, M.; Deerinck, T. J.; Perkins, G. A.; Allen, P. B.; Ellisman, M. H.; Gleeson, J. G., Spinophilin facilitates dephosphorylation of doublecortin by PP1 to mediate microtubule bundling at the axonal wrist. Cell 2007, 129, (3), 579-91, Pubmed
9. * 0003: Broderick, K. E.; Balasubramanian, M.; Chan, A.; Potluri, P.; Feala, J.; Belke, D. D.; McCulloch, A.; Sharma, V. S.; Pilz, R. B.; Bigby, T. D.; Boss, G. R., The cobalamin precursor cobinamide detoxifies nitroprusside-generated cyanide. Exp Biol Med (Maywood) 2007, 232, (6), 789-98, Pubmed
10. * 0003: Campbell, P. H.; Hunt, D.; Jones, Y.; Harwood, F.; Amiel, D.; Omens, J. H.; McCulloch, A. D., Effects of biglycan deficiency on myocardial infarct structure and mechanics. Mol Cell Biomechanics 2008, In Press,
11. * 0001: Cerutti, D. S.; Baker, N. A.; McCammon, J. A., SOLVENT REACTION FIELD POTENTIAL INSIDE AN UNCHARGED GLOBULAR PROTEIN: A BRIDGE BETWEEN IMPLICIT AND EXPLICIT SOLVENT MODELS? J. Chem. Phys. 2007, In Press,
12. * 0001: Chang, C. E.; Trylska, J.; Tozzini, V.; McCammon, J. A., Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chem Biol Drug Des 2007, 69, (1), 5-13, Pubmed
13. 0004: Chang, M. W.; Belew, R. K.; Carroll, K. S.; Olson, A. J.; Goodsell, D. S., Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes. J Comput Chem 2008, Pubmed
14. 0004: Chang, M. W.; Lindstrom, W.; Olson, A. J.; Belew, R. K., Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries. J Chem Inf Model 2007, 47, (3), 1258-62, Pubmed
15. * 0001: Chen, L.; Holst, M. J.; Xu, J. C., The finite element approximation of the nonlinear Poisson-Boltzmann equation. Siam Journal on Numerical Analysis 2007, 45, (6), 2298-2320, ://000253017000002.
16. * 0001: Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A., Ensemble-based Docking Reveals Potential Antiviral Compounds Against Avian Influenza. J Med Chem 2008, In Press,
17. * 0001: Cheng, L. T.; Dzubiella, J.; McCammon, J. A.; Li, B., Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys 2007, 127, (8), 084503, Pubmed
18. * 0001: Cheng, X.; Ivanov, I.; Wang, H.; Sine, S. M.; McCammon, J. A., Nanosecond Time Scale Conformational Dynamics of the Human {alpha}7 Nicotinic Acetylcholine Receptor. Biophys J 2007, Pubmed
19. * 0001: Cheng, Y.; Cheng, X.; Radic, Z.; McCammon, J. A., Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses. J Am Chem Soc 2007, 129, (20), 6562-70, Pubmed
20. * 0001: Cheng, Y.; Suen, J. K.; Radic, Z.; Bond, S. D.; Holst, M. J.; McCammon, J. A., Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models. Biophys Chem 2007, 127, (3), 129-39, Pubmed
21. * 0005: Clementi, L.; Ding, Z.; Krishnan, S.; Wei, X.; Arzberger, P. W.; Li, W. W. In Providing dynamic virtualized access to grid resources via the web 2.0 paradigm, Grid Computing Environment 2007 (GCE 07), Reno, Nevada, 2007; Reno, Nevada, 2007,
22. * 0003: Coppola, B. A.; Covell, J. W.; McCulloch, A. D.; Omens, J. H., Asynchrony of ventricular activation affects magnitude and timing of fiber stretch in late-activated regions of the canine heart. Am J Physiol Heart Circ Physiol 2007, 293, (1), H754-61, Pubmed
23. * 0001: de Oliveira, C. A.; Hamelberg, D.; McCammon, J. A., Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. J Chem Phys 2007, 127, (17), 175105, Pubmed
24. * 0001: de Oliveira, C. A.; Zissen, M.; Mongon, J.; McCammon, J. A., Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket. Curr Pharm Des 2007, 13, (34), 3471-5, Pubmed
25. * 0005: Ding, Z.; Wei, X.; Li, W. W. In VJM-A Deadlock Free Resource CO-allocation Model for Cross Domain Parallel Jobs HPC Asia, Seoul, Korea, 2007; Seoul, Korea, 2007; pp 31-37,
26. * 0005: Ding, Z.; Wei, X.; Luo, Y.; Ma, D.; Arzberger, P. W.; Li, W. W., Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications. New Generation Computing 2007, In Press,
27. * 0005: Ding, Z.; Wei, X.; Tatebe, O.; Papadopoulos, P. M.; Arzberger, P. W.; Li, W. W., Cyberinfrastructure for Biomedical Applications: Metascheduling as Essential Component for Pervasive Computing. In Cyberinfrastructure Technologies and Applications, Cao, J., Ed. Nova Science: 2008; p In Press,
28. * 0001: Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A., PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007, 35, (Web Server issue), W522-5, Pubmed
29. 0001: Dong, F.; Olsen, B.; Baker, N. A., Computational methods for biomolecular electrostatics. Methods Cell Biol 2008, 84, 843-70, Pubmed
30. 0004: Evans, M. J.; Morris, G. M.; Wu, J.; Olson, A. J.; Sorensen, E. J.; Cravatt, B. F., Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides. Mol Biosyst 2007, 3, (7), 495-506, Pubmed
31. * 0003: Feala, J. D.; Coquin, L.; McCulloch, A. D.; Paternostro, G., Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Mol Syst Biol 2007, 3, 99, Pubmed
32. * 0003: Feala, J. D.; Coquin, L.; Paternostro, G.; McCulloch, A. D., Integrating metabolomics and phenomics with systems models of cardiac hypoxia. Prog Biophys Mol Biol 2008, 96, (1-3), 209-25, Pubmed
33. * 0003: Feala, J. D.; Omens, J. H.; Paternostro, G.; McCulloch, A. D., Discovering regulators of the Drosophila cardiac hypoxia response using automated phenotyping technology. Ann N Y Acad Sci 2008, 1123, 169-77, Pubmed
34. 0003: Ferguson, L. R.; Browning, B. L.; Huebner, C.; Petermann, I.; Shelling, A. N.; Demmers, P.; McCulloch, A.; Gearry, R. B.; Barclay, M. L.; Philpott, M., Single nucleotide polymorphisms in human Paneth cell defensin A5 may confer susceptibility to inflammatory bowel disease in a New Zealand Caucasian population. Dig Liver Dis 2008, Pubmed
35. * 0003: Flaim, S. N.; Giles, W. R.; McCulloch, A. D., Arrhythmogenic consequences of Na+ channel mutations in the transmurally heterogeneous mammalian left ventricle: analysis of the I1768V SCN5A mutation. Heart Rhythm 2007, 4, (6), 768-78, Pubmed
36. * 0003: Flaim, S. N.; McCulloch, A. D., Acetylcholine-induced shortening of the epicardial APD may increase repolarization gradients and LQT3 arrhythmic risk. J. Electrocardiol 2007, In Press,
37. 0001: Gorfe, A. A.; Babakhani, A.; McCammon, J. A., MEMBRANE INSERTION FREE ENERGY PROFILE OF H-RAS MEMBRANE ANCHOR. Angewandte Chemie 2007, In Press,
38. * 0001: Gorfe, A. A.; Babakhani, A.; McCammon, J. A., H-RAS PROTEIN IN A BILAYER: INTERACTION AND STRUCTURE PERTURBATION. J. Am. Chem. Society 2007, In Press,
39. * 0001: Gorfe, A. A.; Chang, C. E.; Ivanov, I.; McCammon, J. A., Dynamics of the acetylcholinesterase tetramer. Biophys J 2008, 94, (4), 1144-54, Pubmed
40. * 0001: Gorfe, A. A.; Hanzal-Bayer, M.; Abankwa, D.; Hancock, J. F.; McCammon, J. A., Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem 2007, 50, (4), 674-84, Pubmed
41. * 0001: Grant, B. J.; McCammon, J. A.; Caves, L. S.; Cross, R. A., Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol 2007, 368, (5), 1231-48, Pubmed
42. * 0005: Gupta, N.; Tanner, S.; Jaitly, N.; Adkins, J. N.; Lipton, M.; Edwards, R.; Romine, M.; Osterman, A.; Bafna, V.; Smith, R. D.; Pevzner, P. A., Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res 2007, 17, (9), 1362-77, Pubmed
43. * 0005: Gupta, N.; Tanner, S.; Jaitly, N.; Adkins, J. N.; Lipton, M.; Edwards, R.; Romine, M.; Osterman, A.; Bafna, V.; Smith, R. D.; Pevzner, P. A., Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 2007, 17, (9), 1362-77, Pubmed
44. * 0001: Hamelberg, D.; de Oliveira, C. A.; McCammon, J. A., Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys 2007, 127, (15), 155102, Pubmed
45. 0001: Hamelberg, D.; McCammon, J. A., DEALING WITH BOUND WATERS IN A SITE: DO THEY LEAVE OR STAY? In Computational and Structural Approaches to Drug Discovery, Stroud, R. M., Ed. Royal Society of Chemistry: London, 2007,
46. * 0001: Hamelberg, D.; Shen, T.; McCammon, J. A., A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proc Natl Acad Sci U S A 2007, In Press, Pubmed
47. 0004: Harris, R.; Olson, A. J.; Goodsell, D. S., Automated prediction of ligand-binding sites in proteins. Proteins 2008, 70, (4), 1506-17, Pubmed
48. * 0003: Ingrassia, C.; Usyk, T. P.; Kerckhoffs, R. C.; McCulloch, A. D.; Costa, K. D.; Holmes, J. W., Model-based development of four-dimensional wall motion measures. Computer Methods in Applied Mechanics and Engineering 2007, 196, (31-32), 3061-3069,
49. * 0001: Ivanov, I.; Cheng, X.; Sine, S. M.; McCammon, J. A., Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. J Am Chem Soc 2007, 129, (26), 8217-24, Pubmed
50. 0005: Ju, W. K.; Liu, Q.; Kim, K. Y.; Crowston, J. G.; Lindsey, J. D.; Agarwal, N.; Ellisman, M. H.; Perkins, G. A.; Weinreb, R. N., Elevated hydrostatic pressure triggers mitochondrial fission and decreases cellular ATP in differentiated RGC-5 cells. Invest Ophthalmol Vis Sci 2007, 48, (5), 2145-51, Pubmed
51. * 0003: Kerckhoffs, R. C.; Lumens, J.; Vernooy, K.; Omens, J. H.; Mulligan, L. J.; Delhaas, T.; Arts, T.; McCulloch, A. D.; Prinzen, F. W., Cardiac resynchronization: Insight from experimental and computational models. Prog Biophys Mol Biol 2008, Pubmed
52. 0003: Kerckhoffs, R. C.; McCulloch, A. D., Cardiac Electromechanics in the Healthy Heart. In An Introductory Text to Bioengineering, al, C. e., Ed. World Scientific Publishing Co.: Singapore, 2007; p In Press,
53. * 0003: Kerckhoffs, R. C.; McCulloch, A. D.; Omens, J. H.; Mulligan, L., Effect of pacing site and infarct location on regional mechanics and global hemodynamics in a model based study of heart failure. Lecture Notes in Computer Science 2007, In Press,
54. * 0003: Kerckhoffs, R. C.; Narayan, S. M.; Omens, J. H.; Mulligan, L. J.; McCulloch, A. D., Computational Modeling for bedside application. Heart Failure Clinics 2008, In Press,
55. * 0001: Khavrutskii, I. V.; McCammon, J. A., Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints. J Chem Phys 2007, 127, (12), 124901, Pubmed
56. 0005: Krishnan, S.; Bhatia, K. In SOAs for Scientific Applications: Experiences and Challenges, 3rd IEEE International Conference on e-Science and Grid Computing, Banglore, India, 2008; Banglore, India, 2008,
57. * 0005: Krishnan, S.; Clementi, L.; Ding, Z.; Arzberger, P. W.; Li, W. W., Leveraging the Power of the Grid with Opal: A Guide to Biomedical Application Developers and Users. In Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, Cannataro, M., Ed. Milan, 2008; p Invited,
58. * 0005: Krishnan, S.; Goodman, W.; Clementi, L.; Ding, Z.; ichikawa, K.; Shimojo, S.; Date, S.; Papadopoulos, P.; Smarr, L.; Gilna, P.; Arzberger, P. W.; Li, W. W. In Opal - Enabling the Web 2.0 Paradigm for Biomedical and Metagenomics Applications, PRAGMA 13 Workshop, Urbana-Champaign, Illinois, 2007; Urbana-Champaign, Illinois, 2007,
59. 0001: LeDuc, P. R.; Wong, M. S.; Ferreira, P. M.; Groff, R. E.; Haslinger, K.; Koonce, M. P.; Lee, W. Y.; Love, J. C.; McCammon, J. A.; Monteiro-Riviere, N. A.; Rotello, V. M.; Rubloff, G. W.; Westervelt, R.; Yoda, M., Towards an in vivo biologically inspired nanofactory. Nat Nano 2007, 2, (1), 3-7, Pubmed
60. 0001: Lee, S. J.; Song, Y.; Baker, N. A., Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J 2008, 94, (9), 3565-76, Pubmed
61. * 0003: Li, W.; Gurev, V.; McCulloch, A. D.; Trayanova, N. A., The role of mechanoelectric feedback in vulnerability to electric shock. Prog Biophys Mol Biol 2008, Pubmed
62. * 0001: Lu, B.; Cheng, X.; McCammon, J. A., "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. J Comput Phys 2007, 226, (2), 1348-1366, Pubmed
63. * 0001: Lu, B.; Cheng, X. L.; McCammon, J. A., NEW-VERSION-FAST-MULTIPOLE-METHOD� ACCELERATED ELECTROSTATIC CALCULATIONS IN BIOMOLECULAR SYSTEMS. J. Comput. Phy. 2007, In Press,
64. * 0001: Lu, B.; McCammon, J. A., Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. J. Chem. Theory Comput. 2007, 3, (3), 1134-1142, Pubmed
65. * 0001: Lu, B.; Zhou, Y. C.; Huber, G. A.; Bond, S. D.; Holst, M. J.; McCammon, J. A., Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys 2007, 127, (13), 135102, Pubmed
66. * 0003: Lu, S.; Michailova, A.; Cheng, Y.; Yu, Z.; Kaiser, T. H.; Li, W. W.; Banks, R. E.; Holst, M.; McCammon, J. A.; Hoshijima, M.; McCulloch, A. D., Multi-Scale Modeling of Ventricular Myocytes: Contributions of structural and functional heterogeneities to excitation-contraction coupling in the normal and failing rodent heart. IEEE Engineering in Medicine and Biology 2007,
67. 0005: Martone, M. E.; Tran, J.; Wong, W. W.; Sargis, J.; Fong, L.; Larson, S.; Lamont, S. P.; Gupta, A.; Ellisman, M. H., The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol 2008, 161, (3), 220-31, Pubmed
68. * 0003: Michailova, A.; Lorentz, W.; McCulloch, A., Modeling transmural heterogeneity of K(ATP) current in rabbit ventricular myocytes. Am J Physiol Cell Physiol 2007, 293, (2), C542-57, Pubmed
69. * 0003: Michailova, A.; McCulloch, A. D., Effects of Mg2+, p and PCr on cardiac excitation-metabolic coupling. Magnesium Research 2008, In Press,
70. * 0001: Minh, D. D.; Hamelberg, D.; McCammon, J. A., Accelerated entropy estimates with accelerated dynamics. J Chem Phys 2007, 127, (15), 154105, Pubmed
71. * 0001: Minh, D. D.; McCammon, J. A., SPRINGS AND SPEEDS IN FREE ENERGY RECONSTRUCTION FROM IRREVERSIBLE SINGLE-MOLECULE PULLING EXPERIMENTS. J. Phys. Chem A. 2007, In Press,
72. * 0001: Minh, D. D.; McCammon, J. A., Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments. J Phys Chem B 2007, Pubmed
73. * 0001: Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev, A., Generalized Born Model with a Simple, Robust Molecular Volume Correction. J Chem Theory Comput 2007, 3, 156-169,
74. * 0001: Oliveira, C. A. F.; Zissen, M.; Mongan, J.; McCammon, J. A., MOLECULAR DYNAMICS SIMULATIONS OF METALLOPROTEINASES TYPES 2 AND 3 REVEAL DIFFERENCES IN THE DYNAMIC BEHAVIOR OF THE S1' BINDING POCKET. Curr Pharm Design 2007, In Press,
75. 0004: Olson, A. J.; Hu, Y. H.; Keinan, E., Chemical mimicry of viral capsid self-assembly. Proc Natl Acad Sci U S A 2007, 104, (52), 20731-6, Pubmed
76. 0005: Papadopoulos, P.; Bruno, G.; Katz, M., Beyond Beowulf clusters. ACM Queue 2007, 5, (3), 36-43,
77. 0003: Peter N. Costandi, A. D. M. J. H. O. L. R. F., High-resolution longitudinal MRI of the transition to heart failure. Magnetic Resonance in Medicine 2007, 57, (4), 714-720, Pubmed
78. * 0005: Pezzoli, K.; Tukey, R.; Sarabia, H.; Zaslavsky, I.; Miranda, M. L.; Suk, W. A.; Lin, A.; Ellisman, M., The NIEHS Environmental Health Sciences Data Resource Portal: placing advanced technologies in service to vulnerable communities. Environ Health Perspect 2007, 115, (4), 564-71, Pubmed
79. 0005: Rodriguez, J.; Gupta, N.; Smith, R. D.; Pevzner, P. A., Does trypsin cut before proline? J Proteome Res 2008, 7, (1), 300-5, Pubmed
80. 0001: Schnieders, M. J.; Baker, N. A.; Ren, P.; Ponder, J. W., Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J Chem Phys 2007, 126, (12), 124114, Pubmed
81. * 0001: Sorensen, J.; Hamelberg, D.; Schiott, B.; McCammon, J. A., Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism. Biopolymers 2007, 86, (1), 73-82, Pubmed
82. 0005: Sun, M. G.; Williams, J.; Munoz-Pinedo, C.; Perkins, G. A.; Brown, J. M.; Ellisman, M. H.; Green, D. R.; Frey, T. G., Correlated three-dimensional light and electron microscopy reveals transformation of mitochondria during apoptosis. Nat Cell Biol 2007, 9, (9), 1057-72, Pubmed
83. * 0001: Swanson, J. M.; Wagoner, J. A.; Baker, N. A.; McCammon, J. A., Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned With atom-centered dielectric functions. J Chem Theory Comput 2007, 3, 170-183,
84. * 0001: Tozzini, V.; Trylska, J.; Chang, C. E.; McCammon, J. A., Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007, 157, (3), 606-15, Pubmed
85. Trevor, C.; Chris, S.; Jesus, A. I., MDL, A Domain-Specific Language for Molecular Dynamics. In Proceedings of the 40th Annual Simulation Symposium, IEEE Computer Society: 2007; pp 256-266.
86. * 0001: Trylska, J.; Tozzini, V.; Chang, C. E.; McCammon, J. A., HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys J 2007, 92, (12), 4179-87, Pubmed
87. * 0001: Xie, L.; Wang, J.; Bourne, P. E., In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Comput Biol 2007, 3, (11), 2324-2332,
88. 0004: Xu, L.; Chong, Y.; Hwang, I.; D'Onofrio, A.; Amore, K.; Beardsley, G. P.; Li, C.; Olson, A. J.; Boger, D. L.; Wilson, I. A., Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase. J Biol Chem 2007, 282, (17), 13033-46, Pubmed
89. 0004: Xu, L.; Chong, Y.; Hwang, I.; D'Onofrio, A.; Amore, K.; Beardsley, G. P.; Li, C.; Olson, A. J.; Boger, D. L.; Wilson, I. A., Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase. J Biol Chem 2007, 282, (17), 13033-46, Pubmed
90. 0005: Xuong, N. H.; Jin, L.; Kleinfelder, S.; Li, S.; Leblanc, P.; Duttweiler, F.; Bouwer, J. C.; Peltier, S. T.; Milazzo, A. C.; Ellisman, M., Future directions for camera systems in electron microscopy. Methods Cell Biol 2007, 79, 721-39, Pubmed
91. * 0001: Yu, Z.; Hayashi, T.; Cheng, Y.; Holst, M. J.; McCammon, J. A.; Hoshijima, M.; Michailova, A.; McCulloch, A. D.; Li, W. W.; Arzberger, P. W. In Multi-Scale Modeling of 3D Cardiac Myocytes: Image Analysis, Geometric Processing, and Numerical Simulation Biophysical Society Meeting, Long Beach, CA, 2008; Long Beach, CA, 2008,
92. * 0001: Yu, Z.; Holst, M. J.; Cheng, Y.; McCammon, J. A., Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model 2008, Pubmed
93. 0005: Zemljic-Harpf, A. E.; Miller, J. C.; Henderson, S. A.; Wright, A. T.; Manso, A. M.; Elsherif, L.; Dalton, N. D.; Thor, A. K.; Perkins, G. A.; McCulloch, A. D.; Ross, R. S., Cardiac-Myocyte Specific Excision of the Vinculin Gene Disrupts Cellular Junctions Causing Sudden Death or Dilated Cardiomyopathy. Mol Cell Biol 2007, Pubmed
94. * 0003: Zhang, Y.; Sekar, R. B.; McCulloch, A. D.; Tung, L., Cell cultures as models of cardiac mechanoelectric feedback. Prog Biophys Mol Biol 2008, Pubmed
95. * 0004: Zhao, Y.; Sanner, M. F., FLIPDock: docking flexible ligands into flexible receptors. Proteins 2007, 68, (3), 726-37, Pubmed
96. * 0004: Zhao, Y.; Sanner, M. F., Protein-ligand docking with multiple flexible side chains. J Comput Aided Mol Des 2007, Pubmed
97. * 0005: Zheng, C.; Katz, M.; Papadopoulos, P.; Abramson, D.; Ayyub, S.; Enticott, C.; Garic, S.; Goscinski, W.; Arzberger, P. W.; Lee, B. S.; Phatanapherom, S.; Sriprayoonsakul, S.; Uthayopas, P.; Tanaka, Y.; Tanimura, Y., Lessons Learned through driving science applications in the PRAGMA grid. IJWGS 2007, 3, (3), 287-312,
98. * 0001: Zhou, Y. C.; Holst, M.; McCammon, J. A., A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces. Journal of Mathematical Analysis and Applications 2008, 340, (1), 135-164, ://000252860500012.
99. * 0001: Zhou, Y. C.; Lu, B.; Huber, G. A.; Holst, M. J.; McCammon, J. A., Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B 2008, 112, (2), 270-5, Pubmed
100. 0001: Aksoylu, B.; Holst, M., Optimality of multilevel preconditioners for local mesh refinement in three dimensions. SIAM J. Numer. Anal. 2006, 44, 1005-1025,
101. * 0005: Bailey, T. L.; Williams, N.; Misleh, C.; Li, W. W., MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34, (Web Server Issue), W369-73,
102. * 0078: Baitaluk, M.; Qian, X.; Godbole, S.; Raval, A.; Ray, A.; Gupta, A., PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics 2006, 7, 55, Pubmed
103. * 0002: Baitaluk, M.; Sedova, M.; Ray, A.; Gupta, A., BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res 2006, 34, (Web Server issue), W466-71, Pubmed
104. * 0005: Baldridge, K. K.; Sudholt, W.; Greenberg, J. P.; Amoreira, C.; Potier, Y.; Altintas, I.; Birnbaum, A.; Abramson, D.; Enticott, C.; Slavisa, G., Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry. In Parallel Computing for Bioinformatics Zomaya, A. Y., Ed. John Wiley & Sons: 2006; p In Press,
105. 0005: Bhatia, K.; Stearn, B.; Taufer, M.; Zamudio, R.; Catarino, D. In Extending Grid Protocols onto the Desktop using the Mozilla Framework, Grid Computing Environment, Tampa, Florida, 2006; Tampa, Florida, 2006; p In Press,
106. 0005: Bourque, G.; Tesler, G.; Pevzner, P. A., The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res 2006, 16, (3), 311-3, Pubmed
107. 0005: Bouwer, J. C.; Mackey, M. R.; Lawrence, A.; Deerinck, T. J.; Jones, Y. Z.; Terada, M.; Martone, M. E.; Peltier, S. T.; Ellisman, M. H., The application of energy-filtered electron microscopy to tomography of thick, selectively stained biological samples. Methods Cell Biol 2007, 79, 643-60, Pubmed
108. * 0003: Broderick, K. E.; Feala, J.; McCulloch, A.; Paternostro, G.; Sharma, V. S.; Pilz, R. B.; Boss, G. R., The nitric oxide scavenger cobinamide profoundly improves survival in a Drosophila melanogaster model of bacterial sepsis. Faseb J 2006, 20, (11), 1865-73, Pubmed
109. * 0001: Bui, J. M.; McCammon, J. A., Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc Natl Acad Sci U S A 2006, 103, (42), 15451-6, Pubmed
110. 0003: Camelliti, P.; Gallagher, J.; Kohl, P.; McCulloch, A. D., Micropatterned cell cultures on elastic membranes as an in-vitro model of myocardium. Nature Protocols 2006, 1, (3), 1379-1391,
111. * 0001: Cerutti, D. S.; Jain, T.; McCammon, J. A., CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci 2006, 15, (7), 1579-96, Pubmed
112. 0005: Chaisson, M. J.; Raphael, B. J.; Pevzner, P. A., Microinversions in mammalian evolution. Proc Natl Acad Sci U S A 2006, 103, (52), 19824-9, Pubmed
113. * 0001: Chen, L.; Holst, M., Mesh Adaptation Based on Optimal Delaunay Triangulation. SIAM J. Sci. Comp. 2006, Submitted,
114. * 0001: Chen, L.; Holst, M.; Xu, J., Convergence and Optimality of Adaptive Mixed Finite Element Methods. Math. Comp. 2006, Submitted,
115. * 0001: Chen, L.; Holst, M.; Xu, J., Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation. SIAM J. Numer. Anal. 2006, Submitted,
116. 0078: Chen, L.; Martone, M. E.; Gupta, A.; Fong, L.; Wong-Barnum, M. In OntoQuest: Exploring Ontological Data Made Easy., VLDB 2006, 2006; 2006; pp 1183-1186,
117. * 0001: Cheng, X.; Wang, H.; Grant, B.; Sine, S. M.; McCammon, J. A., Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors. PLoS Comput Biol 2006, 2, (9), e134, Pubmed
118. * 0001: Cheng, Y.; Suen, J. K.; Zhang, D.; Bond, S. D.; Zhang, Y.; Song, Y.; Baker, N. A.; Bajaj, C. L.; Holst, M. J.; McCammon, J. A., Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J 2007, 92, (10), 3397-406, Pubmed
119. * 0003: Costandi, P. N.; Frank, L. R.; McCulloch, A. D.; Omens, J. H., Role of Diastolic Properties in the Transition to Failure in a Mouse Model of Cardiac Dilatation. Am J Physiol Heart Circ Physiol 2006, 291, (6), H2971-2979, Pubmed
120. 0003: Costandi, P. N.; McCulloch, A. D.; Omens, J. H.; Frank, L. R., High-resolution longitudinal MRI of the transition to heart failure. Magn Reson Med 2007, 57, (4), 714-20, Pubmed
121. 0005: De Jaco, A.; Comoletti, D.; Kovarik, Z.; Gaietta, G.; Radic, Z.; Lockridge, O.; Ellisman, M. H.; Taylor, P., A mutation linked with autism reveals a common mechanism of endoplasmic reticulum retention for the alpha,beta-hydrolase fold protein family. J Biol Chem 2006, 281, (14), 9667-76, Pubmed
122. * 0001: de Oliveira, C. A.; Hamelberg, D.; McCammon, J. A., On the application of accelerated molecular dynamics to liquid water simulations. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 2006, 110, (45), 22695-701, Pubmed
123. 0005: DeClue, M. S.; Baldridge, K. K.; Kast, P.; Hilvert, D., Experimental and computational investigation of the uncatalyzed rearrangement and elimination reactions of isochorismate. J Am Chem Soc 2006, 128, (6), 2043-51, Pubmed
124. * 0005: Ding, Z.; Luo, Y.; Wei, X.; Misleh, C.; Li, W. W.; Arzberger, P. W.; Tatebe, O. In My WorkSphere: Integrative Work Environment for Grid-unaware Biomedical Researchers and Applications, Supercomputing Conference 2006, SC06, 2nd Grid Computing Environment Workshop, Tampa, Florida, 2006; Tampa, Florida, 2006; p In Press,
125. * 0001: Dzubiella, J.; Swanson, J. M.; McCammon, J. A., Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys Rev Lett 2006, 96, (8), 087802, Pubmed
126. * 0001: Dzubiella, J.; Swanson, J. M.; McCammon, J. A., Coupling nonpolar and polar solvation free energies in implicit solvent models. J Chem Phys 2006, 124, (8), 084905, Pubmed
127. * 0005: Eskin, E.; Sharan, R.; Halperin, E., A note on phasing long genomic regions using local haplotype predictions. J Bioinform Comput Biol 2006, 4, (3), 639-47, Pubmed
128. * 0004: Eubanks, L. M.; Rogers, C. J.; Beuscher, A. E. t.; Koob, G. F.; Olson, A. J.; Dickerson, T. J.; Janda, K. D., A molecular link between the active component of marijuana and Alzheimer's disease pathology. Mol Pharm 2006, 3, (6), 773-7, Pubmed
129. 0003: Feala, J.; Coquin, L.; McCulloch, A. D.; Paternostro, G., Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Mol. Systems Biol 2007, In Press,
130. * 0003: Flaim, S. N.; Giles, W. R.; McCulloch, A. D., Contributions of Sustained INa and IKv43 to Transmural Heterogeneity of Early Repolarization and Arrhythmogenesis in Canine Left Ventricular Myocytes. Am J Physiol Heart Circ Physiol 2006, 291, (6), H2617-2629, Pubmed
131. * 0001: Giorgione, J. R.; Lin, J. H.; McCammon, J. A.; Newton, A. C., Increased membrane affinity of the C1 domain of protein kinase C delta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem 2006, 281, (3), 1660-9, Pubmed
132. * 0001: Gorfe, A. A.; Hanzal-Bayer, M.; Abankwa, D.; Hancock, J. F.; McCammon, J. A., Structure and Dynamics of the Full-Length Lipid-Modified H-Ras Protein in a 1,2-Dimyristoylglycero-3-phosphocholine Bilayer. J Med Chem 2007, 50, (4), 674-684, Pubmed
133. * 0001: Grant, B. J.; Rodrigues, A. P.; Elsawy, K. M.; McCammon, J. A.; Caves, L. S., Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 2006, 22, (21), 2695-2696, Pubmed
134. * 0001: Gullingsrud, J.; Kim, C.; Taylor, S. S.; McCammon, J. A., Dynamic binding of PKA regulatory subunit RI alpha. Structure 2006, 14, (1), 141-9, Pubmed
135. * 0001: Hamacher, K.; Hubsch, A.; McCammon, J. A., A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys 2006, 124, (16), 164907, Pubmed
136. * 0001: Hamacher, K.; Trylska, J.; McCammon, J. A., Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput Biol 2006, 2, (2), e10, Pubmed
137. * 0001: Hamelberg, D.; Shen, T.; McCammon, J. A., Insight into the role of hydration on protein dynamics. J Chem Phys 2006, 125, (9), 094905, Pubmed
138. * 0005: Hamura, T.; Ibusuki, Y.; Uekusa, H.; Matsumoto, T.; Siegel, J. S.; Baldridge, K. K.; Suzuki, K., Dodecamethoxy- and hexaoxotricyclobutabenzene: synthesis and characterization. J Am Chem Soc 2006, 128, (31), 10032-3, Pubmed
139. 0004: Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S., A semiempirical free energy force field with charge-based desolvation. J Comput Chem 2007, 28, (6), 1145-1152, Pubmed
140. * 0003: Hunter, P. J.; Li, W. W.; McCulloch, A. D.; Noble, D., Multi-scale Modeling Standards, Tools, Databases for the Physiome Project. Computer 2006, 39, (11), 48-54,
141. 0005: Ichikawa, K.; Date, S.; Krishnan, S.; Li, W. W.; Nakata, K.; Yonezawa, Y.; Nakamura, H.; Shimojo, S. In OPAL OP: An Extensible Grid-Enabling Wrapping Tool For Legacy Applications, 3rd International Workshop on Grid Computing & Applications (GCA2007), Singapore, 2007; Singapore, 2007; p In Press,
142. * 0001: Ivanov, I.; Chapados, B. R.; McCammon, J. A.; Tainer, J. A., Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res 2006, 34, (20), 6023-6033, Pubmed
143. * 0001: Ivanov, I.; Tainer, J. A.; McCammon, J. A., Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A 2007, 104, (5), 1465-70, Pubmed
144. * 0001: Ivanov, I.; Vemparala, S.; Pophristic, V.; Kuroda, K.; DeGrado, W. F.; McCammon, J. A.; Klein, M. L., Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics. J Am Chem Soc 2006, 128, (6), 1778-9, Pubmed
145. * 0001: Jain, T.; Cerutti, D. S.; McCammon, J. A., Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci 2006, 15, (9), 2029-39, Pubmed
146. * 0004: Jiang, Z.; Georgel, P.; Li, C.; Choe, J.; Crozat, K.; Rutschmann, S.; Du, X.; Bigby, T.; Mudd, S.; Sovath, S.; Wilson, I. A.; Olson, A.; Beutler, B., Details of Toll-like receptor:adapter interaction revealed by germ-line mutagenesis. Proc Natl Acad Sci U S A 2006, 103, (29), 10961-6, Pubmed
147. 0005: Jones, N. C.; Pevzner, P. A., Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics 2006, 22, (14), e236-42, Pubmed
148. 0003: Kerckhoffs, R. C.; Healy, S. N.; Usyk, T. P.; McCulloch, A. D. In Computational methods for modeling cardiac electromechanics, Proc IEEE, 2006; 2006; pp 1-15,
149. * 0003: Kerckhoffs, R. C.; Neal, M. L.; Gu, Q.; Bassingthwaighte, J. B.; Omens, J. H.; McCulloch, A. D., Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation. Ann Biomed Eng 2007, 35, (1), 1-18, Pubmed
150. * 0003: Konecny, R.; Trylska, J.; Tama, F.; Zhang, D.; Baker, N. A.; Brooks, C. L., 3rd; McCammon, J. A., Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2006, 82, (2), 106-20, Pubmed
151. 0005: Krishnan, S.; Stearn, B.; Bhatia, K.; Baldridge, K. K.; Li, W. W.; Arzberger, P. W. In Opal: Simple Web Services Wrapers for Scientific Applications, International Conference of Web Services, Chicago, USA, 2006; Chicago, USA, 2006; pp 823-832,
152. * 0005: Lathers, A.; Su, M.; Kulungowski, A.; Lin, A. W.; Mehta, G.; Peltier, S. T.; Deelman, E.; Ellisman, M. H. In Enabling Parallel Scientific Applications with Workflow Tools, Proceedings of the 6th International Workshop on Challenges of Large Applications in Distributed Environments, 2006; 2006; pp 55-60,
153. * 0005: Lawrence, A.; Bouwer, J. C.; Perkins, G.; Ellisman, M. H., Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J Struct Biol 2006, 154, (2), 144-67, Pubmed
154. * 0001: Lewis, J. A.; Mongan, J.; McCammon, J. A.; Cohen, S. M., Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor. ChemMedChem 2006, 1, (7), 694-7, Pubmed
155. * 0005: Li, W. W.; Baker, N. A.; Baldridge, K.; McCammon, J. A.; Ellisman, M. H.; Gupta, A.; Holst, M. J.; McCulloch, A. D.; Michailova, A.; Papadopoulos, P.; Olson, A.; Sanner, M.; Arzberger, P. W., National Biomedical Computation Resource (NBCR): Devloping End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research In CTWatch Quarterly, Stevens, R. C., Ed. 2006; Vol. 2, pp 6-17, Pubmed
156. 0005: Li, W. W.; Krishnan, S.; Mueller, K.; Ichikawa, K.; Date, S.; Dallakyan, S.; Sanner, M. F.; Misleh, C.; Ding, Z.; Wei, X.; Tatebe, O.; Arzberger, P. W. In Building Cyberinfrastructure for Bioinformatics Using Service Oriented Architecture, the 6th IEEE International Symposium on Cluster Computing & the Grid, Singapore, 2006; Singapore, 2006; pp 39-46,
157. * 0003: Lorenzen-Schmidt, I.; Schmid-Schonbein, G. W.; Giles, W. R.; McCulloch, A. D.; Chien, S.; Omens, J. H., Chronotropic response of cultured neonatal rat ventricular myocytes to short-term fluid shear. Cell Biochem Biophys 2006, 46, (2), 113-22, Pubmed
158. * 0001: Lu, B.; Cheng, X.; Huang, J.; McCammon, J. A., Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A 2006, 103, (51), 19314-9, Pubmed
159. * 0005: Marchini, J.; Cutler, D.; Patterson, N.; Stephens, M.; Eskin, E.; Halperin, E.; Lin, S.; Qin, Z. S.; Munro, H. M.; Abecasis, G. R.; Donnelly, P., A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 2006, 78, (3), 437-50, Pubmed
160. 0003: McCulloch, A. D.; Arzberger, P. W.; Hunter, P. J., Computational Physiology: From Genome to Physiome. The Physiologist 2006, 49, (1), 94-95,
161. * 0003: McCulloch, A. D.; Omens, J. H., Myocyte shearing, myocardial sheets, and microtubules. Circ Res 2006, 98, (1), 1-3, Pubmed
162. T 0003: Michailova, A. P.; Lorentz, W.; McCulloch, A. D., Modeling transmural heterogeneity of KATP current in rabbit ventricular myocytes. Am J Physiol Cell Physiol 2007, In Press, Pubmed
163. * 0001: Minh, D. D.; Chang, C. E.; Trylska, J.; Tozzini, V.; McCammon, J. A., The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics. J Am Chem Soc 2006, 128, (18), 6006-6007, Pubmed
164. * 0001: Ngo, J. C.; Gullingsrud, J.; Giang, K.; Yeh, M. J.; Fu, X. D.; Adams, J. A.; McCammon, J. A.; Ghosh, G., SR protein kinase 1 is resilient to inactivation. Structure 2007, 15, (1), 123-33, Pubmed
165. 0005: Onuchic, J. N.; Kobayashi, C.; Miyashita, O.; Jennings, P.; Baldridge, K. K., Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci 2006, 361, (1472), 1439-43, Pubmed
166. * 0005: O'Rourke, S.; Chechik, G.; Friedman, R.; Eskin, E., Discrete profile comparison using information bottleneck. BMC Bioinformatics 2006, 7 Suppl 1, S8, Pubmed
167. * 0001: Perryman, A. L.; Lin, J. H.; McCammon, J. A., Restrained molecular dynamics simulations of HIV-1 protease: The first step in validating a new target for drug design. Biopolymers 2006, 82, (3), 272-84, Pubmed
168. * 0005: Pezzoli, K.; Tukey, R.; Sarabia, H.; Zaslavsky, I. N.; Miranda, M. L.; Suk, W. A.; Lin, A.; Ellisman, M. H., The NIEHS Environmental Health Sciences Data Resource Portal: Placing Advanced Technologies in Service to Vulnerable Communities. 2006, In Press,
169. * 0003: Saucerman, J. J.; McCulloch, A. D., Cardiac beta-Adrenergic Signaling: From Subcellular Microdomains to Heart Failure. Ann N Y Acad Sci 2006, 1080, 348-61, Pubmed
170. * 0001: Senapati, S.; Cheng, Y.; McCammon, J. A., In-situ Synthesis of a Tacrine-Triazole-Based Inhibitor of Acetylcholinesterase: Configurational Selection Imposed by Steric Interactions. J Med Chem 2006, 49, (21), 6222-6230, Pubmed
171. * 0001: Shen, T.; Hamelberg, D.; McCammon, J. A., Elasticity of peptide omega bonds. Phys Rev E Stat Nonlin Soft Matter Phys 2006, 73, (4 Pt 1), 041908, Pubmed
172. * 0001: Sorensen, J.; Hamelberg, D.; Schiott, B.; McCammon, J. A., Comparative molecular dynamics analysis of the stability of Transthyretin providing insight into the fibrillation mechanism. Biopolymers 2007, In Press, Pubmed
173. 0005: Terraneo, G.; Potenza, D.; Canales, A.; Jimenez-Barbero, J.; Baldridge, K. K.; Bernardi, A., A Simple Model System for the Study of Carbohydrate-Aromatic Interactions. J Am Chem Soc 2007, 129, (10), 2890-2900, Pubmed
174. * 0001: Ung, M. U.; Lu, B.; McCammon, J. A., E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Biopolymers 2006, 81, (6), 428-39, Pubmed
175. * 0001: Vigil, D.; Lin, J. H.; Sotriffer, C. A.; Pennypacker, J. K.; McCammon, J. A.; Taylor, S. S., A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP. Protein Sci 2006, 15, (1), 113-21, Pubmed
176. * 0001: Wagoner, J. A.; Baker, N. A., Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. Proc Natl Acad Sci U S A 2006, 103, (22), 8331-6, Pubmed
177. * 0004: Whiting, M.; Muldoon, J.; Lin, Y. C.; Silverman, S. M.; Lindstrom, W.; Olson, A. J.; Kolb, H. C.; Finn, M. G.; Sharpless, K. B.; Elder, J. H.; Fokin, V. V., Inhibitors of HIV-1 protease by using in situ click chemistry. Angew Chem Int Ed Engl 2006, 45, (9), 1435-9, Pubmed
178. 0004: Whiting, M.; Tripp, J. C.; Lin, Y. C.; Lindstrom, W.; Olson, A. J.; Elder, J. H.; Sharpless, K. B.; Fokin, V. V., Rapid discovery and structure-activity profiling of novel inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(I)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization. J Med Chem 2006, 49, (26), 7697-710, Pubmed
179. 0005: Wilmarth, P. A.; Tanner, S.; Dasari, S.; Nagalla, S. R.; Riviere, M. A.; Bafna, V.; Pevzner, P. A.; David, L. L., 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? J Proteome Res 2006, 5, (10), 2554-66, Pubmed
180. 0005: Wu, Y. T.; Hayama, T.; Baldridge, K. K.; Linden, A.; Siegel, J. S., Synthesis of fluoranthenes and indenocorannulenes: elucidation of chiral stereoisomers on the basis of static molecular bowls. J Am Chem Soc 2006, 128, (21), 6870-84, Pubmed
181. * 0001: Yang, G.; Trylska, J.; Tor, Y.; McCammon, J. A., Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies. J Med Chem 2006, 49, (18), 5478-90, Pubmed
182. * 0005: Ye, C.; Eskin, E., Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Bioinformatics 2007, 23, (2), e84-90, Pubmed
183. * 0001: Zhang, D.; Gullingsrud, J.; McCammon, J. A., Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc 2006, 128, (9), 3019-26, Pubmed
184. * 0001: Zhang, X.; Bajaj, C. L.; Kwon, B.; Dolinsky, T. J.; Nielsen, J. E.; Baker, N. A., Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Model Simulations 2006, 5, 1196-1213,
185. * 0004: Zhao, Y.; Stoffler, D.; Sanner, M., Hierarchical and multi-resolution representation of protein flexibility. Bioinformatics 2006, 22, (22), 2768-74, Pubmed
186. 0005: Zhi, D.; Krishna, S. S.; Cao, H.; Pevzner, P.; Godzik, A., Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics 2006, 7, 460, Pubmed
187. * 0005: Zhi, D.; Raphael, B. J.; Price, A. L.; Tang, H.; Pevzner, P. A., Identifying repeat domains in large genomes. Genome Biol 2006, 7, (1), R7, Pubmed
188. * 0005: Abramson, D.; Lynch, A.; Takemaya, H.; Tanimura, Y.; Date, S.; Nakmura, H.; Jeong, K.; Hwang, S.; Zhu, J.; Lu, Z.-h.; Amoreira, C.; Baldridge, K. K.; Lee, H.-C.; Wang, C.-W.; Shih, H.-L.; Molina, T.; Li, W. W.; Arzberger, P. W. In Deploying Scientific Applications to the PRAGMA Grid testbed: Strategies and Lessons, Sixth IEEE International Symposium on Cluster Computing and the Grid, 2006. CCGrid 06., Singapore, 2006; Singapore, 2006; pp 241-248,
189. * 0001: Adcock, S. A.; McCammon, J. A., Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 2006, 106, (5), 1589-615, Pubmed
190. 0005: Akiyama, T.; Teranishi, Y.; Nozaki, K.; Kato, S.; Shimojo, S.; Peltier, S. T.; Lin, A.; Molina, T.; Yang, G.; Lee, D.; Ellisman, M.; Naito, S.; Koike, A.; Matsumoto, S.; Yoshida, K.; Mori, H., Scientific Grid Activities and PKI Deployment in the Cybermedia Center, Osaka University. J Clin Monit Comput 2005, 19, (4-5), 279-94, Pubmed
191. 0018: Ashihara, T.; Trayanova, N. A., Cell and tissue responses to electric shocks. Europace 2005, 7 Suppl 2, 155-65, Pubmed
192. * 0088: Baitaluk, M.; Qian, X.; Godbole, S.; Raval, A.; Ray, A.; Gupta, A., PathSys: Integrating Molecular Interaction Graphs for Systems Biology. BMC Bioinformatics 2005, In Press,
193. 0005: Baldridge, K. K.; Bhatia, K.; Greenberg, J. P.; Stearn, B.; Mock, S.; Sudholt, W.; Krishnan, S.; Bowne, A.; Amoreira, C.; Potier, Y. In Grid-Enabled Molecular Science through Online Networked Environments, Life Sciences Grid Workshop, Singapore, 2005; World Scientific Press: Singapore, 2005,
194. 0005: Baldridge, K. K.; Sudholt, W.; Greenberg, J. P.; Amoreira, C.; Potier, Y.; Altintas, I.; Birnbaum, A.; Abramson, D.; Enticott, C.; Slavisa, G., Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry. . In Parallel Computing for Bioinformatics, Zomaya, A. Y., Ed. John Wiley & Sons: 2005; p In Press,
195. * 0005: Bhatia, K.; Chandra, S.; Mueller, K. In GAMA: Grid Account Management Architecture, 1st IEEE International Conference on e- Science and Grid Computing, Melbourne, Australia, 2006; Melbourne, Australia, 2006; p In Press,
196. 0108: Brik, A.; Alexandratos, J.; Lin, Y. C.; Elder, J. H.; Olson, A. J.; Wlodawer, A.; Goodsell, D. S.; Wong, C. H., 1,2,3-triazole as a peptide surrogate in the rapid synthesis of HIV-1 protease inhibitors. Chembiochem 2005, 6, (7), 1167-9, Pubmed
197. 0107: Briknarova, K.; Nasertorabi, F.; Havert, M. L.; Eggleston, E.; Hoyt, D. W.; Li, C.; Olson, A. J.; Vuori, K.; Ely, K. R., The serine-rich domain from Crk-associated substrate (p130cas) is a four-helix bundle. J Biol Chem 2005, 280, (23), 21908-14, Pubmed
198. * 0001: Bui, J. M.; Radic, Z.; Taylor, P.; McCammon, J. A., Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase. Biophys J 2006, 90, (9), 3280-7, Pubmed
199. 0020: Camelliti, P.; McCulloch, A. D.; Kohl, P., Microstructured cocultures of cardiac myocytes and fibroblasts: a two-dimensional in vitro model of cardiac tissue. Microsc Microanal 2005, 11, (3), 249-59, Pubmed
200. * 0001: Cerutti, D. S.; Ten Eyck, L. F.; McCammon, J. A., Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. J. Chem. Theory Comput. 2005, 1, 143-152,
201. * 0001: Chang, C. E.; Shen, T.; Trylska, J.; Tozzini, V.; McCammon, J. A., Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model. Biophys J 2006, 90, (11), 3880-5, Pubmed
202. * 0088: Chen, L.; Gupta, A.; Kurul, M. E. In Stack-based Algorithms for Pattern Matching on DAGs, Int. Conf. on Very Large Databases (VLDB), Trondheim, Norway, 2005; Trondheim, Norway, 2005; p In Press,
203. * 0088: Chen, L.; Gupta, A.; Kurul, M. E. In A semantic-aware RDF query algebra, 12th Int. Conf. on Mgmnt of Data (COMAD), Hyderabad, India, Dec 2005, 2005; Hyderabad, India, 2005; p In Press,
204. * 0001: Cheng, X.; Lu, B.; Grant, B.; Law, R. J.; McCammon, J. A., Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol 2006, 355, (2), 310-24, Pubmed
205. * 0001: Cheng, Y.; Zhang, Y.; McCammon, J. A., How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc 2005, 127, (5), 1553-62, Pubmed
206. * 0001: Cheng, Y.; Zhang, Y.; McCammon, J. A., How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Sci 2006, 15, (4), 672-83, Pubmed
207. 0038: Coggan, J. S.; Bartol, T. M.; Esquenazi, E.; Stiles, J. R.; Lamont, S.; Martone, M. E.; Berg, D. K.; Ellisman, M. H.; Sejnowski, T. J., Evidence for ectopic neurotransmission at a neuronal synapse. Science 2005, 309, (5733), 446-51, Pubmed
208. * 21: Costa, S.; Feala, J.; Colajanni, M.; McCulloch, A. D.; Paternostro, G., Network properties of aging genes and of genes changing in expression during aging. Bioinformatics 2006, Submitted,
209. 0106: de Parseval, A.; Chatterji, U.; Morris, G.; Sun, P.; Olson, A. J.; Elder, J. H., Structural mapping of CD134 residues critical for interaction with feline immunodeficiency virus. Nat Struct Mol Biol 2005, 12, (1), 60-6, Pubmed
210. 0104: Dickerson, T. J.; Beuscher, A. E. t.; Rogers, C. J.; Hixon, M. S.; Yamamoto, N.; Xu, Y.; Olson, A. J.; Janda, K. D., Discovery of acetylcholinesterase peripheral anionic site ligands through computational refinement of a directed library. Biochemistry 2005, 44, (45), 14845-53, Pubmed
211. * 0001: Dzubiella, J.; McCammon, J. A., Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J Chem Phys 2005, 122, (18), 184902, Pubmed
212. * 0001: Gao, F.; Bren, N.; Burghardt, T. P.; Hansen, S.; Henchman, R. H.; Taylor, P.; McCammon, J. A.; Sine, S. M., Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem 2005, 280, (9), 8443-51, Pubmed
213. Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease: Grethe, J. S.; Baru, C.; Gupta, A.; James, M.; Ludaescher, B.; Martone, M. E.; Papadopoulos, P. M.; Peltier, S. T.; Rajasekar, A.; Santini, S.; Zaslavsky, I. N.; Ellisman, M. H., Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud Health Technol Inform 2005, 112, 100-9, Pubmed
214. * 0001: Hamelberg, D.; McCammon, J. A., Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc 2005, 127, (40), 13778-9, Pubmed
215. * 0001: Hamelberg, D.; Shen, T.; McCammon, J. A., Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J Am Chem Soc 2005, 127, (6), 1969-74, Pubmed
216. * 0001: Hamelberg, D.; Shen, T.; McCammon, J. A., Relating kinetic rates and local energetic roughness by accelerated molecular dynamics simulations. J. Chem. Phys. 2005, 122, 241103,
217. * 0003: Healy, S. N.; McCulloch, A. D., An ionic model of stretch-activated and stretch-modulated currents in rabbit ventricular myocytes. Europace 2005, 7 Suppl 2, 128-34, Pubmed
218. Encyclopedia of Life Sciences 0001: Henchman, R. H.; McCammon, J. A., Protein structural flexibility: molecular motions. John Wiley and Nature Publishing Group: 2005; p In Press,
219. * 0078: Henchman, R. H.; Wang, H. L.; Sine, S. M.; Taylor, P.; McCammon, J. A., Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J 2005, 88, (4), 2564-76, Pubmed
220. 0039: Hoffmann, C.; Gaietta, G.; Bunemann, M.; Adams, S. R.; Oberdorff-Maass, S.; Behr, B.; Vilardaga, J. P.; Tsien, R. Y.; Ellisman, M. H.; Lohse, M. J., A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat Methods 2005, 2, (3), 171-6, Pubmed
221. * 0003: Kerckhoffs, R. C. P.; Healy, S. N.; Usyk, T. P.; McCulloch, A. D., Computational Methods for Cardiac Electromechanics. 2005, In Press,
222. * 0095: Konecny, R.; Trylska, J.; Tama, F.; Zhang, D.; Baker, N. A.; Brooks, C. L., 3rd; McCammon, J. A., Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2005, In Press, Pubmed
223. * 0005: Krishnan, S.; Baldridge, K. K.; Greenberg, J. P.; Stearn, B.; Bhatia, K. In An end-to-end web services-based infrastructure for biomedical applications, Grid 2005, Seattle, Washington, 2005; Seattle, Washington, 2005; p In Press,
224. Krishnan, S.; Stearn, B.; Bhatia, K.; Greenberg, J. P.; Li, W. W.; Arzberger, P. W.; Baldridge, K. K. Web services-based data integration for life science computations; SDSC Technical Report: 2005; pp TR-2005-2.
225. * 0001: Law, R. J.; Henchman, R. H.; McCammon, J. A., A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 2005, 102, (19), 6813-8, Pubmed
226. * 0005: Lawrence, A.; Bouwer, J. C.; Perkins, G. A.; Ellisman, M. H., Transform based backprojection for volume reconstruction of large format electron microscope tilt series. J Struc. Biol. 2005, In Press,
227. * 0005: Li, W. W.; Arzberger, P. W.; Yeo, C. L.; Ang, L.; Tatebe, O.; Sekiguchi, S.; Jeong, K.; Hwang, S.; Date, S.; Kwak, J.-H. In Proteome Analysis using iGAP in Gfarm, The Second International Life Science Grid Workshop 2005, Grid Asia 2005, Singapore, 2005; World Scientific Press: Grid Asia 2005, Singapore, 2005,
228. * 0005: Li, W. W.; Yeo, C. L.; Jeong, K.; Hwang, S.; Date, S.; Kwak, J.; Sekiguchi, S.; Ang, L.; Arzberger, P. W. In Proteome Analysis using iGAP in Gfarm., Life Sciences Grid Workshop, Singapore, 2005; Singapore, 2005; p In Press,
229. * 0005: Lin, A. W.; Dai, L.; Mock, J.; Peltier, S.; Ellisman, M. H. In The Telescience Tools: Version 2.0, The 1st IEEE International Conference on e-Science and Grid Computing, Melbourne, Australia, 2005; Melbourne, Australia, 2005; pp 56-63,
230. 0005: Lin, A. W.; Dai, L.; Ung, K.; Peltier, S.; Ellisman, M. H. In The Telescience Project: Applications to Middleware Interaction Components, The 18th IEEE International Symposium on Computer-Based Medical Systems, Dublin, Ireland, 2005; Dublin, Ireland, 2005; pp 543-548,
231. 0101: Lorenzen-Schmidt, I.; McCulloch, A. D.; Omens, J. H., Deficiency of actinin-associated LIM protein alters regional right ventricular function and hypertrophic remodeling. Ann Biomed Eng 2005, 33, (7), 888-96, Pubmed
232. 0101: Lorenzen-Schmidt, I.; Stuyvers, B. D.; ter Keurs, H. E.; Date, M. O.; Hoshijima, M.; Chien, K. R.; McCulloch, A. D.; Omens, J. H., Young MLP deficient mice show diastolic dysfunction before the onset of dilated cardiomyopathy. J Mol Cell Cardiol 2005, 39, (2), 241-50, Pubmed
233. * 0001: Lu, B.; Cheng, X.; Hou, T.; McCammon, J. A., Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J Chem Phys 2005, 123, (8), 84904, Pubmed
234. * 0094: Lu, B.; Wong, C. F.; McCammon, J. A., Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Protein Sci 2005, 14, (1), 159-68, Pubmed
235. * 0001: Lu, B.; Zhang, D.; McCammon, J. A., Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys 2005, 122, (21), 214102, Pubmed
236. 0105: Marshall, T. G.; Lee, R. E.; Marshall, F. E., Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b. Theoretical Biol. Medical Modelling 2006, 3, (1), In Press, Pubmed
237. * 0001: McCammon, J. A., Computation of Non-covalent Binding Affinities. In Theory and Applications of Computational Chemistry, Dykstra, C.; Frenking, G.; Kim, K.; Scuseria, G., Eds. Elsevier: Amsterdam, 2005; pp 41-46,
238. * 0001: McCammon, J. A., Target flexibility in molecular recognition. Biochim Biophys Acta 2005, 1754, (1-2), 221-224, Pubmed
239. * 0001: McCammon, J. A.; Wade, R. C., Pushing the limits: Editorial overview. Curr. Opin. Struct. Biol. 2005, 15, 135-136,
240. * 0021: McCulloch, A. D.; Paternostro, G., Cardiac systems biology. Ann N Y Acad Sci 2005, 1047, 283-95, Pubmed
241. Active pixel sensor array as a detector for electron microscopy: Milazzo, A. C.; Leblanc, P.; Duttweiler, F.; Jin, L.; Bouwer, J. C.; Peltier, S.; Ellisman, M.; Bieser, F.; Matis, H. S.; Wieman, H.; Denes, P.; Kleinfelder, S.; Xuong, N. H., Active pixel sensor array as a detector for electron microscopy. Ultramicroscopy 2005, 104, (2), 152-9, Pubmed
242. * 0112: Mills, R. W.; Narayan, S. M.; McCulloch, A. D., Mechanisms of Conduction Slowing During Myocardial Stretch by Ventricular Volume Loading 2006, Submitted,
243. * 0001: Minh, D. D.; Bui, J. M.; Chang, C. E.; Jain, T.; Swanson, J. M.; McCammon, J. A., The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2. Biophys J 2005, In Press, Pubmed
244. * 0001: Puerta, D. T.; Mongan, J.; Tran, B. L.; McCammon, J. A.; Cohen, S. M., Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc 2005, 127, (41), 14148-9, Pubmed
245. 0018: Rodriguez, B.; Eason, J. C.; Trayanova, N., Differences between left and right ventricular anatomy determine the types of reentrant circuits induced by an external electric shock. A rabbit heart simulation study. Prog Biophys Mol Biol 2005, In Press, Pubmed
246. 0018: Rodriguez, B.; Li, L.; Eason, J. C.; Efimov, I. R.; Trayanova, N. A., Differences between left and right ventricular chamber geometry affect cardiac vulnerability to electric shocks. Circ Res 2005, 97, (2), 168-75, Pubmed
247. 0005: Sacerdoti, F. D.; Katz, M. J.; Papadopoulos, P. M. In 411 on Scalable Password Service, IEEE High Performance Distributed Computing Service, North Carolina, 2005; IEEE Computer Society: North Carolina, 2005; p In Press, Pubmed
248. Proteomics and Bioinformatics 0004: Sanner, M. F.; Stolz, M.; Burkhard, P.; Kong, X.-P.; Min, G.; Sun, T.-t.; Driamov, S.; Aebi, U.; Stoffler, D., Visualizing Nature at Work from the Nano to the Macro Scale. John Wiley & sons, Ltd.: 2005; Vol. 1, p 7-11,
249. 0103: Santelli, E.; Leone, M.; Li, C.; Fukushima, T.; Preece, N. E.; Olson, A. J.; Ely, K. R.; Reed, J. C.; Pellecchia, M.; Liddington, R. C.; Matsuzawa, S., Structural analysis of Siah1-Siah-interacting protein interactions and insights into the assembly of an E3 ligase multiprotein complex. J Biol Chem 2005, 280, (40), 34278-87, Pubmed
250. 50: Sarraf, C. E.; Harris, A. B.; McCulloch, A. D.; Eastwood, M., Cell proliferation rates in an artificial tissue-engineered environment. Cell Prolif 2005, 38, (4), 215-21, Pubmed
251. * Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes`: Saucerman, J. J.; Zhang, J.; Stenbit, A., E.; Tsien, R. Y.; McCulloch, A. D., Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes`. 2006, Submitted,
252. * 0001: Senapati, S.; Bui, J. M.; McCammon, J. A., Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a Molecular Dynamics Study. J Med Chem 2005, 48, (26), 8155-62, Pubmed
253. * 0098: Shen, T.; Zong, C.; Hamelberg, D.; McCammon, J. A.; Wolynes, P. G., The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. Faseb J 2005, 19, (11), 1389-95, Pubmed
254. * 0094: Sims, P. A.; Wong, C. F.; Vuga, D.; McCammon, J. A.; Sefton, B. M., Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. J Comput Chem 2005, 26, (7), 668-81, Pubmed
255. Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography: Sosinsky, G. E.; Deerinck, T. J.; Greco, R.; Buitenhuys, C. H.; Bartol, T. M.; Ellisman, M. H., Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography. Neuroinformatics 2005, 3, (2), 133-62, Pubmed
256. * 0001: Swanson, J. M.; Adcock, S. A.; McCammon, J. A., Optimized radii for Poisson-Boltzmann calculations with the AMBER force field. J. Chem. Theory Comput. 2005, 1, 484-493,
257. * 0001: Tozzini, V.; McCammon, J. A., A coarse grained model for the dynamics of the early stages of the binding mechanism of HIV-1 Protease. Chem. Phys. Letters 2005, 413, 123-128,
258. 0018: Trayanova, N., In pursuit of the elusive culprit. Heart Rhythm 2005, 2, (7), 729-30, Pubmed
259. * 0097: Trylska, J.; McCammon, J. A.; Brooks Iii, C. L., Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc 2005, 127, (31), 11125-33, Pubmed
260. * 0001: Trylska, J.; Tozzini, V.; McCammon, J. A., Exploring global motions and correlations in the ribosome. Biophys J 2005, 89, (3), 1455-63, Pubmed
261. * 0001: Ung, M. U.; Lu, B.; McCammon, J. A., E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Biopolymers 2005, In Press, Pubmed
262. 0102: Vajragupta, O.; Boonchoong, P.; Morris, G. M.; Olson, A. J., Active site binding modes of curcumin in HIV-1 protease and integrase. Bioorg Med Chem Lett 2005, 15, (14), 3364-8, Pubmed
263. 0001: Wagoner, J.; Baker, N. A., Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J. Comput. Chem 2005, 25, 1623-1629,
264. * 0005: Wei, X.; Ding, Z.; Li, W. W.; Tatebe, O.; Jiang, J.; Hu, L.; Arzberger, P. W. In GDIA: A Scalable Grid Infrastructure for Data Intensive Applications, IEEE International Conference on Hybrid Information Technology, ICHIT 2006, Cheju Island, Korea, 2006; IEEE Computer Society: Cheju Island, Korea, 2006; p Accepted,
265. 0101: Weis, S. M.; Zimmerman, S. D.; Shah, M.; Covell, J. W.; Omens, J. H.; Ross, J., Jr.; Dalton, N.; Jones, Y.; Reed, C. C.; Iozzo, R. V.; McCulloch, A. D., A role for decorin in the remodeling of myocardial infarction. Matrix Biol 2005, 24, (4), 313-24, Pubmed
266. * 0001: Wong, C. F.; Kua, J.; Zhang, Y.; Straatsma, T. P.; McCammon, J. A., Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins 2005, 61, (4), 850-8, Pubmed
267. * 0011: Yerushalmi, R.; Brandis, A.; Rosenbach-Belkin, V.; Baldridge, K. K.; Scherz, A., Modulation of Fragmental Charge Transfer via Hydrogen Bonds. Direct Measurement of Electronic Contributions. J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory 2006, 110, (2), 412-21, Pubmed
268. * 0005: Zaitlen, N. A.; Kang, H. M.; Feolo, M. L.; Sherry, S. T.; Halperin, E.; Eskin, E., Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP. Genome Res 2005, 15, (11), 1594-600, Pubmed
269. * 0001: Zhang, D.; McCammon, J. A., The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis. PLoS Comput Biol 2005, 1, (6), e62, Pubmed
270. 0001: Aksoylu, B.; Bond, S.; Holst, M. J., Local Refinement and Multilevel Preconditioning III: Implementation and numerical experiments. SIAM J.Sci. Comput. 2004, 25, (2), 478-498,
271. 0001: Aksoylu, B.; Holst, M. J., Local Refinement and Multilevel Preconditioning I: Optimality of the BPX Preconditioner. SIAM J. Numer. Anal. 2004, In Press,
272. 0001: Aksoylu, B.; Holst, M. J., Local Refinement and Multilevel Preconditioning II: Stabilizing Hierachical Basis Methods SIAM J. Numer. Anal., on Locally Refined Meshes. SIAM J. Numer. Anal. 2004, In Press,
273. * 0077: Baldridge, K. K.; Greenberg, J. P.; Sudholt, W.; Altintas, I.; Bhatia, K.; Mock, S.; Amoreira, C.; Potier, Y., The Computational Chemistry Prototyping Environment. IEEE on Grid Computing 2005, 93, (Special Issue), 510,
274. Handbook of Numerical Analysis 0003: Belik, M. E.; Usyk, T. P.; McCulloch, A. D., Computational methods for cardiac electrophysiology. Elsevier: 2004; Vol. Computational Models for the Human Body, p 69,
275. 0035, 0070: Bossy-Wetzel, E.; Talantova, M. V.; Lee, W. D.; Scholzke, M. N.; Harrop, A.; Mathews, E.; Gotz, T.; Han, J.; Ellisman, M. H.; Perkins, G. A.; Lipton, S. A., Crosstalk between nitric oxide and zinc pathways to neuronal cell death involving mitochondrial dysfunction and p38-activated K+ channels. Neuron 2004, 41, (3), 351-65, Pubmed
276. 0005: Bouwer, J. C.; Mackey, M. R.; Lawrence, A.; Deerinck, T. J.; Jones, Y. Z.; Terada, M.; Martone, M. E.; Peltier, S.; Ellisman, M. H., Automated most-probable loss tomography of thick selectively stained biological specimens with quantitative measurement of resolution improvement. J Struct Biol 2004, 148, (3), 297-306, Pubmed
277. 0005: Bruno, G.; Katz, M.; Sacerdoti, F. D.; Papadopoulos, P. M. In Rolls: Modifying a Standard System Installer to Support User-Customizable Cluster Frontend Appliances, IEEE International Conference on Cluster Computing, San Diego, USA, 2004; San Diego, USA, 2004; pp 421-430, Pubmed
278. * 0001: Bui, J. M.; Tai, K.; McCammon, J. A., Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc 2004, 126, (23), 7198-205, Pubmed
279. * 0088: Chen, L.; Gupta, A.; Kurul, M. E. In Efficient Algorithms for Pattern Matching on Directed Acyclic Graphs IEEE Int. Conf. on Data Engineering (ECDE), Tokyo, Japan, March, 2005, 2005; Tokyo, Japan, 2005,
280. 0051: Chen, L.; McCulloch, A. D.; May-Newman, K., Nonhomogeneous deformation in the anterior leaflet of the mitral valve. Ann Biomed Eng 2004, 32, (12), 1599-606, Pubmed
281. * 0001: Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A., PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 2004, 32, (Web Server issue), W665-7, Pubmed
282. 0001: Estep, D.; Holst, M. J.; Larson, M., Generalized Green's functions and the effective domain of influence. SIAM J. Sci. Comp. 2005, 26, (4), 1314-1339,
283. 0001: Fenwick, J.; Bank, R.; Holst, M. J. In Meshing a Simple Polygon in an Arbitrary Plane using Triangle Fans, International Meshing Roundtable, San Diego, 2004; San Diego, 2004,
284. 0021: Ferrarini, L.; Bertelli, L.; Feala, J.; McCulloch, A. D.; Paternostro, G., A more efficient search strategy for aging genes based on connectivity. Bioinformatics 2005, 21, (3), 338-48, Pubmed
285. 0004: Gillet, A.; Sanner, M.; Stoffler, D.; Olson, A., Tangible augmented interfaces for structural molecular biology. IEEE Comput Graph Appl 2005, 25, (2), 13-7, Pubmed
286. 0004: Gillet, A.; Sanner, M.; Stoffler, D.; Olson, A., Tangible interfaces for structural molecular biology. Structure (Camb) 2005, 13, (3), 483-91, Pubmed
287. * 0006: Greenberg, J. P.; Mock, S.; Bhatia, K.; Katz, M.; Bruno, G.; Papadopoulos, P.; Baldridge, K. K., Incorporation of Middleware and Grid Technologies to Enhance Usability in Computational Chemistry Applications. Future Generations of Computer Systems 2005, 21, 3-10,
288. * 0001: Hamelberg, D.; McCammon, J. A., Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc 2004, 126, (24), 7683-9, Pubmed
289. * 0001: Hamelberg, D.; Mongan, J.; McCammon, J. A., Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys 2004, 120, (24), 11919-29, Pubmed
290. 0069: Healy, S. N.; Belik, M. E.; Michailova, A.; Puglisi, J. L.; Bers, D. M.; McCulloch, A. D. In 3D Simulation of Action Potential Heterogeneity in Rabbit Ventricular Tissue, Biophysical Society, Long Beach, CA, 2004; Long Beach, CA, 2004; p 299a,
291. Nature Encyclopedia of Life Sciences 0001: Henchman, R. H.; McCammon, J. A., Protein structural flexibility: molecular motions. Macmillan Publishers: 2004; p In Press,
292. * 0004: Huey, R.; Goodsell, D. S.; Morris, G. M.; Olson, A. J., Grid-based hydrogen bond potentials with improved directionality. Lett. Drug Des. & Disc 2004, 1, 178-183,
293. 0088: Martone, M. E.; Gupta, A.; Ellisman, M. H., E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 2004, 7, (5), 467-72, Pubmed
294. * 0003: Michailova, A.; Saucerman, J.; Belik, M. E.; McCulloch, A. D., Modeling regulation of cardiac KATP and L-type Ca2+ currents by ATP, ADP, and Mg2+. Biophys J 2005, 88, (3), 2234-49, Pubmed
295. 0003: Michailova, A. P.; Belik, M. E.; McCulloch, A. D., Effects of magnesium on cardiac excitation-contraction coupling. J Am Coll Nutr 2004, 23, (5), 514S-517S, Pubmed
296. * 0001: Perryman, A. L.; Lin, J. H.; McCammon, J. A., 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 Sci 2004, 13, (4), 1108-23, Pubmed
297. 0073, 0035: Ricci, J. E.; Munoz-Pinedo, C.; Fitzgerald, P.; Bailly-Maitre, B.; Perkins, G. A.; Yadava, N.; Scheffler, I. E.; Ellisman, M. H.; Green, D. R., Disruption of mitochondrial function during apoptosis is mediated by caspase cleavage of the p75 subunit of complex I of the electron transport chain. Cell 2004, 117, (6), 773-86, Pubmed
298. 0005: Sacerdoti, F. D.; Chandra, S.; Bhatia, K. In Grid Systems Deployment & Management Using Rocks, IEEE International Conference on Cluster Computing, San Diego, USA, 2004; IEEE Computer Society: San Diego, USA, 2004; pp 337-345, Pubmed
299. * 0004: Sanner, M. F., A component-based software environment for visualizing large macromolecular assemblies. Structure (Camb) 2005, 13, (3), 447-62, Pubmed
300. * 0003, 0069: Saucerman, J. J.; Healy, S. N.; Belik, M. E.; Puglisi, J. L.; McCulloch, A. D., Proarrhythmic consequences of a KCNQ1 AKAP-binding domain mutation: computational models of whole cells and heterogeneous tissue. Circ Res 2004, 95, (12), 1216-24, Pubmed
301. 0003: Saucerman, J. J.; McCulloch, A. D., Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation. Prog Biophys Mol Biol 2004, 85, (2-3), 261-78, Pubmed
302. 0001: Schames, J. R.; Henchman, R. H.; Siegel, J. S.; Sotriffer, C. A.; Ni, H.; McCammon, J. A., Discovery of a novel binding trench in HIV integrase. J Med Chem 2004, 47, (8), 1879-81, Pubmed
303. * 0001: Senapati, S.; Wong, C. F.; McCammon, J. A., Finite concentration effects on diffusion-controlled reactions. J Chem Phys 2004, 121, (16), 7896-900, Pubmed
304. * 0001: Sims, P. A.; Wong, C. F.; McCammon, J. A., Charge optimization of the interface between protein kinases and their ligands. J Comput Chem 2004, 25, (11), 1416-29, Pubmed
305. * 0001: Song, Y.; Zhang, Y.; Shen, T.; Bajaj, C. L.; McCammon, J. A.; Baker, N. A., Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J 2004, 86, (4), 2017-29, Pubmed
306. * 0005: Sudholt, W.; Baldridge, K.; Abramson, D.; Enticott, C.; Garic, S., Parameter Scan of an Effective Group Difference Pseudopotential Using Grid Computing. New Generation Computing 2004, 22, 125-135,
307. 0077: Sudholt, W.; Baldridge, K. K.; Abramson, D.; Enticott, C.; Garic, S., Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential. In Lecture Notes in Computer Science, Springer-Verlag: Heidelberg, 2004; Vol. 3036, pp 148-155,
308. 0077: Sudholt, W.; Baldridge, K. K.; Abramson, D.; Enticott, C.; Garic, S.; Kondric, C.; Nguyen, D., Application of Grid Computing to Parameter Sweeps and Optimizations in Molecular Modeling. Future Generation Computer Systems. Future Generations of Computer Systems 2005, 21, 27-35,
309. * 0001: Swanson, J. M.; Henchman, R. H.; McCammon, J. A., Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J 2004, 86, (1 Pt 1), 67-74, Pubmed
310. 0001: Trylska, J.; Grochowski, P.; McCammon, J. A., The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. Protein Sci 2004, 13, (2), 513-28, Pubmed
311. * 0001: Trylska, J.; Konecny, R.; Tama, F.; Brooks, C. L., 3rd; McCammon, J. A., Ribosome motions modulate electrostatic properties. Biopolymers 2004, 74, (6), 423-31, Pubmed
312. * 0019: Xie, F.; Qu, Z.; Yang, J.; Baher, A.; Weiss, J. N.; Garfinkel, A., A simulation study of the effects of cardiac anatomy in ventricular fibrillation. J Clin Invest 2004, 113, (5), 686-93, Pubmed
313. * 0004, 0027: Xu, L.; Li, C.; Olson, A. J.; Wilson, I. A., Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening. J Biol Chem 2004, 279, (48), 50555-65, Pubmed
314. * 0001, 0010: Yerushalmi, R.; Scherz, A.; Baldridge, K. K., Direct experimental evaluation of charge scheme performance by a molecular charge-meter. J Am Chem Soc 2004, 126, (18), 5897-905, Pubmed
315. * 0001: Zhang, D.; Konecny, R.; Baker, N. A.; McCammon, J. A., 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 2004, 75, (4), 325-37, Pubmed
316. * 0001, 0078: Zhang, D.; Suen, J.; Zhang, Y.; Song, Y.; Radic, Z.; Taylor, P.; Holst, M. J.; Bajaj, C.; Baker, N. A.; McCammon, J. A., Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J 2005, 88, (3), 1659-65, Pubmed

Award Period II (5/1/1999 - 4/30/2004)


This Resource is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant (P 41 RR08605) to researchers at the University of California, San Diego, including the San Diego Supercomputer Center (SDSC), the California Institute of Telecommunications and Information Technology (Calit2), The Center for Research in Biological Systems (CRBS), The Scripps Research Institute (TSRI), and Washington University in St. Louis (WUSTL).

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