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1. Singh A, Nguyen M, Purawat S, Crawl D, Altintas I, (2018), "Modular Resource Centric Learning for Workflow Performance Prediction", CoRR, 17 Apr 2018, abs/1711.05: November 15, 2017
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2. Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE, (2018), "Determinants of Oligonucleotide Selectivity of APOBEC3B", Journal of Chemical Information and Modeling, August 21, 2018: August 21, 2018, (DOI: 10.1021/acs.jcim.8b00427).
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3. Venkatramani A, Ricci CG, Oldfield E, McCammon JA, (2018), "Remarkable similarity in P. falciparum and P. vivax Geranylgeranyl Diphosphate Synthase (GGPPS) dynamics and its implication for anti-malarial drug design", Biophysical Journal, 114, 3: pg: 49a, 2 February 2018, (DOI: 10.1016/j.bpj.2017.11.322).
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4. Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro RE, Wang Z, Aihara H, (2018), "The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release", Journal of Biological Chemistry, April 6, 2018, 293, 21: pg: 7969-7981, May 25, 2018, (DOI: 10.1074/jbc.RA118.002503).
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5. Amaro RE, Baudry J, Chodera J, Demir O, McCammon JA, Miao Y, Smith JC, (2018), "Ensemble Docking in Drug Discovery", BIOPHYSICAL PERSPECTIVE, 22 May 2018, 114, 10: pg: 2271-2278, 20 February 2018, (DOI: 10.1016/j.bpj.2018.02.038).
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6. Amaro RE, Mulholland AJ, (2018), "Multiscale methods in drug design bridge chemical and biological complexity in the search for cures", Nature Reviews Chemistry, 2, 4: 11 April 2018, (DOI: 10.1038/s41570-018-0148).
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7. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA, (2018), "Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.", Frontiers in Molecular Biosciences, 5, 13: 12 Feb 2018, (DOI: 10.3389/fmolb.2018.00013).
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8. Miao Y, McCammon JA, (2018), "Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor", Proc. Natl. Acad. Sci. USA, March 5, 2018, 115, 12: pg: 3036-3041, March 20, 2018, (DOI: 10.1073/pnas.1800756115).
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9. Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA, (2018), "Ligand Binding Pathways and Conformational Transitions of the HIV Protease", Biochemistry, 2018 Mar 6, 57, 9: pg: 1533–1541, 2018 Feb 15, (DOI: 10.1021/acs.biochem.7b01248).
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10. Lee CT, Amaro RE, (2018), "Exascale Computing: A New Dawn for Computational Biology", Computing in Science & Engineering, 30 August 2018, 20, 5: pg: 18-25, (DOI: 10.1109/MCSE.2018.05329812).
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11. Mermelstein DJ, Lin C, Nelson G, Kretsch R1, McCammon JA, Walker RC, (2018), "Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package", J Comput Chem, 2018 Mar 12: (DOI: 10.1002/jcc.25187).
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12. Mulero MC, Shahabi S, Ko MS, Schiffer JM, Huang D, Wang VY, Amaro RE, Huxford T, Ghosh G, (2018), "Protein co-factors are essential for high affinity DNA binding by the nuclear factor κB RelA subunit", Biochemistry, April 30, 2018, 57, 20: pg: 2943–2957, 2018 May 22, (DOI: 10.1021/acs.biochem.8b00158).
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13. Gilbert K, Forsch N, Hegde S, Mauger C, Omens JH, Perry JC, Pontré B, Suinesiaputra A, Young AA, McCulloch AD, (2018), "Atlas-Based Computational Analysis of Heart Shape and Function in Congenital Heart Disease", Journal of Cardiovascular Translational Research, 02 January 2018, 11, 2: pg: 123-132, (DOI: 10.1007/s12265-017-9778-5).
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14. Jagger BR, Lee CT, Amaro RE, (2018), "Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach", J. Phys. Chem. Lett., August 2, 2018, 9, 17: pg: 4941–4948, (DOI: 10.1021/acs.jpclett.8b02047).
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15. Wagner J, Demir O, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE, (2018), "Determinants of Substrate Specificity in APOBEC3B": May 4, 2018, (DOI: 10.26434/chemrxiv.6217427.v1).
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16. Huang YM, McCammon JA, Miao Y, (2018), "Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation", J. Chem. Theory Comp., February 28, 2018, 14, 4: pg: 1853-1864, (DOI: 10.1021/acs.jctc.7b01226).
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17. Fang F, Huang J, Huber G, McCammon JA, Zhang B, (2018), "Hierarchical Orthogonal Matrix Generation and Matrix-Vector Multiplications in Rigid Body Simulations.", SIAM J. Sci. Comput., 10 May 2018, 40, 3: pg: A1345–A1361, (DOI: 10.1137/17M1117744).
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18. Erdemir A, Hunter PJ, Holzapfel GA, Loew LM, Middleton J, Jacobs CR, Nithiarasu P, Löhner R, Wei G, Winkelstein BA, Barocas VH, Guilak F, Ku JP, Hicks JL, Delp SL, Sacks M, Weiss JA, Ateshian GA, Maas SA, McCulloch AD, Peng GCY, (2018), "Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research", J Biomech Eng, 2017/12/17, 140, 2: pg: 11, 2018 Feb 1, 1528-8951 (Electronic) 0148-0731 (Linking), (DOI: 10.1115/1.4038768).
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19. Haberl MG, Churas C, Tindall L, Phan S, Bushong EA, Akay R, Deerinck TJ Peltier ST, Ellisman MH, (2018), "CDeep3M - Plug-and-Play cloud based deep learning for image segmentation of light, electron and X-ray microscopy.", Nature Methods: 2018
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20. Lye TH, Vincent KP, McCulloch AD, Hendon CP, (2018), "Tissue-specific optical mapping models of swine atria informed by optical coherence tomography", Biophys J, 114, 6: pg: 1477-1489, 27 March 2018, (DOI: 10.1016/j.bpj.2018.01.035).
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21. Lewalle A, Land S, Carruth E, Frank LR, Lamata P, Omens JH, McCulloch AD, Niederer SA, Smith NP, (2018), "Decreasing compensatory ability of concentric ventricular hypertrophy in aortic-banded rat hearts", Front Physiol - Comp Physiol Med, 9: 2018 Feb 23, (DOI: 10.3389/fphys.2018.00037).
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22. Cranford JP, O’Hara TJ, Villongco CT, Hafez OM, Blake RC, Loscalzo J, Fattebert J-L, Richards DF, Zhang X, Glosli JN, McCulloch AD, Krummen DE, Lightstone FC, Wong SE, (2018), "Efficient Computational Modeling of Human Ventricular Activation and its Electrocardiographic Representation: A Sensitivity Study", Cardiovasc Eng Tech, 16 March 2018: pg: 1-21, Print 1869-408X Online 1869-4098, (DOI: 10.1007/s13239-018-0347-0).
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23. Schiffer JM, Luo M, Dommer AC, Thoron G, Pendergraft M, Santander MV, Lucero D, Pecora de Barros E, Prather KA, Grassian VH, Amaro RE, (2018), "Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols", J. Phys. Chem. Lett., June 19, 2018, 9, 14: pg: 3839-3849, (DOI: 10.1021/acs.jpclett.8b01363).
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24. Salamango DJ, McCann JL, Demir O, Brown WL, Amaro RE, Harris RS, (2018), "APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces", Journal of Molecular Biology, 430, 17: pg: 2695-2708, 17 August 2018, (DOI: 10.1016/j.jmb.2018.04.044).
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25. Alok Singh, Arvind Rao, Shweta Purawat, Ilkay Altintas, (2017), "A machine learning approach for modular workflow performance prediction", ACM, Proceedings: pg: 7, November 12, 2017, (DOI: 10.1145/3150994.3150998).
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26. Andersen, O. J., Risor, M. W., Poulsen, E. C., Nielsen, N. C., Miao, Y., Enghild, J. J., Schiott, B., (2017), "Reactive Center Loop Insertion in alpha-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation", Biochemistry: Jan 17, 1520-4995 (Electronic) 0006-2960 (Linking), (DOI: 10.1021/acs.biochem.6b00839).
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27. Andrew Gillette, Michael Holst, Yunrong Zhu, (2017), "FINITE ELEMENT EXTERIOR CALCULUS FOR EVOLUTION PROBLEMS.", Journal of Computational Mathematics, 35, 2: pg: 187-212, March 1, 2017, (DOI: 10.4208/jcm.1610-m2015-0319).
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28. Caliman, A. D., Miao, Y., McCammon, J. A., (2017), "Activation mechanisms of the first sphingosine-1-phosphate receptor", Protein Sci, 26, 6: pg: 1150-1160, Jun, 1469-896X (Electronic) 0961-8368 (Linking), (DOI: 10.1002/pro.3165).
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29. Shi, K., Carpenter, M. A., Banerjee, S., Shaban, N. M., Kurahashi, K., Salamango, D. J., McCann, J. L., Starrett, G. J., Duffy, J. V., Demir, O., Amaro, R. E., Harki, D. A., Harris, R. S., Aihara, H., (2017), "Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B", Nat Struct Mol Biol, Nature Structural & Molecular Biology, 24, 2: pg: 131-139, 19 December 2016, 1545-9993, (DOI: 10.1038/nsmb.3344).
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30. Caliman, A. D., Miao, Y., McCammon, J. A., (2017), "Mapping the allosteric sites of the A2A adenosine receptor", Chem Biol Drug Des: Jun 22, 1747-0285 (Electronic) 1747-0277 (Linking), (DOI: 10.1111/cbdd.13053).
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31. Chan, A. H., Yi, S. W., Weiner, E. M., Amer, B. R., Sue, C. K., Wereszczynski, J., Dillen, C. A., Senese, S., Torres, J. Z., McCammon, J. A., Miller, L. S., Jung, M. E., Clubb, R. T., (2017), "NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors", Chem Biol Drug Des, 90, 3: pg: 327-344, Sep, 1747-0285 (Electronic) 1747-0277 (Linking), (DOI: 10.1111/cbdd.12962).
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32. Cheng, K. J., Demir, O., Amaro, R. E., (2017), "A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases", Genes (Basel), 8, 6: pg: 166, June 20, 2017, 2073-4425 (Print) 2073-4425 (Linking), (DOI: 10.3390/genes8060166).
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33. Churas, C., Perez, A. J., Hakozaki, H., Wong, W., Lee, D., Peltier, S. T., Ellisman, M. H., (2017), "Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections", Bioinformatics, 33, 19: pg: 3145-3147, Oct 1, 1367-4803, (DOI: 10.1093/bioinformatics/btx376).
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34. Churas, C., Perez, A. J., Hakozaki, H., Wong, W., Lee, D., Peltier, S. T., Ellisman, M. H., (2017), "Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections", Bioinformatics, 2017/09/29, 33, 19: pg: 3145-3147, Oct 1, 1367-4811 (Electronic) 1367-4803 (Linking), (DOI: 10.1093/bioinformatics/btx376).
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35. Dewan, S., Krishnamurthy, A., Kole, D., Conca, G., Kerckhoffs, R., Puchalski, M. D., Omens, J. H., Sun, H., Nigam, V., McCulloch, A. D., (2017), "Model of Human Fetal Growth in Hypoplastic Left Heart Syndrome: Reduced Ventricular Growth Due to Decreased Ventricular Filling and Altered Shape", Front Pediatr, 5: pg: 25, 2296-2360 (Print) 2296-2360 (Linking), (DOI: 10.3389/fped.2017.00025).
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36. Dewan, S., McCabe, K. J., Regnier, M., McCulloch, A. D., (2017), "Insights and Challenges of Multi-Scale Modeling of Sarcomere Mechanics in cTn and Tm DCM Mutants-Genotype to Cellular Phenotype", Front Physiol, 8: pg: 151, 1664-042X (Print) 1664-042X (Linking), (DOI: 10.3389/fphys.2017.00151).
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37. Dick, B. L., Patel, A., McCammon, J. A., Cohen, S. M., (2017), "Effect of donor atom identity on metal-binding pharmacophore coordination", J Biol Inorg Chem, 22, 4: pg: 605-613, Jun, 1432-1327 (Electronic) 0949-8257 (Linking), (DOI: 10.1007/s00775-017-1454-3).
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38. Falkenberg, C. V., Azeloglu, E. U., Stothers, M., Deerinck, T. J., Chen, Y., He, J. C., Ellisman, M. H., Hone, J. C., Iyengar, R., Loew, L. M., (2017), "Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability", PLoS Comput Biol, 13, 3: pg: e1005433, Mar, 1553-7358 (Electronic) 1553-734X (Linking), (DOI: 10.1371/journal.pcbi.1005433).
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39. Gaieb, Z., Liu, S., Gathiaka, S., Chiu, M., Yang, H., Shao, C., Feher, V. A., Walters, W. P., Kuhn, B., Rudolph, M. G., Burley, S. K., Gilson, M. K., Amaro, R. E., (2017), "D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies", J Comput Aided Mol Des, 2017/12/06: Dec 4, 1573-4951 (Electronic) 0920-654X (Linking), (DOI: 10.1007/s10822-017-0088-4).
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40. Gan, Z., Powell, F. L., Zambon, A. C., Buchholz, K. S., Fu, Z., Ocorr, K., Bodmer, R., Moya, E. A., Stowe, J. C., Haddad, G. G., McCulloch, A. D., (2017), "Transcriptomic analysis identifies a role of PI3K-Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo", J Physiol, 595, 17: pg: 5797-5813, Sep 01, 1469-7793 (Electronic) 0022-3751 (Linking), (DOI: 10.1113/JP274556).
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41. Grogan, F., Holst, M., Lindblom, L., Amaro, R., (2017), "Reliability Assessment for Large-Scale Molecular Dynamics Approximations", The Journal of chemical physics, 20 December 2017, 147, 23: December 2017, (DOI: 10.1063/1.5009431).
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42. Herum, K. M., Choppe, J., Kumar, A., Engler, A. J., McCulloch, A. D., (2017), "Mechanical regulation of cardiac fibroblast profibrotic phenotypes", Mol Biol Cell, 28, 14: pg: 1871-1882, Jul 07, 1939-4586 (Electronic) 1059-1524 (Linking), (DOI: 10.1091/mbc.E17-01-0014).
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43. Herum, K. M., Lunde, I. G., McCulloch, A. D., Christensen, G., (2017), "The Soft- and Hard-Heartedness of Cardiac Fibroblasts: Mechanotransduction Signaling Pathways in Fibrosis of the Heart", J Clin Med, 6, 5: May 19, 2077-0383 (Print) 2077-0383 (Linking), (DOI: 10.3390/jcm6050053).
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44. Hirakis, S. P., Malmstrom, R. D., Amaro, R. E., (2017), "Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism", Biochemistry, June 29, 2017, 56, 30: pg: 3885-3888, 1520-4995 (Electronic) 0006-2960 (Linking), (DOI: 10.1021/acs.biochem.7b00461).
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45. Jaremko, M. J., Lee, D. J., Patel, A., Winslow, V., Opella, S. J., McCammon, J. A., Burkart, M. D., (2017), "Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins", Biochemistry, 2017/09/19, 56, 40: pg: 5269-5273, Oct 10, 1520-4995 (Electronic) 0006-2960 (Linking), (DOI: 10.1021/acs.biochem.7b00884).
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46. Huang, Y. M., Huber, G. A., Wang, N., Minteer, S. D., McCammon, J. A., (2017), "Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling", Protein Sci, 2017/11/03: Nov 2, 1469-896X (Electronic) 0961-8368 (Linking), (DOI: 10.1002/pro.3338).
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47. Ho, G., Villongco, C. T., Yousefian, O., Bradshaw, A., Nguyen, A., Faiwiszewski, Y., Hayase, J., Rappel, W. J., McCulloch, A. D., Krummen, D. E., (2017), "Rotors exhibit greater surface ECG variation during ventricular fibrillation than focal sources due to wavebreak, secondary rotors, and meander", J Cardiovasc Electrophysiol, 28, 10: pg: 1158-1166, Oct, 1540-8167 (Electronic) 1045-3873 (Linking), (DOI: 10.1111/jce.13283).
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48. Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., Krasny, R., Wei, G. W., Holst, M. J., McCammon, J. A., Baker, N. A., (2017), "Improvements to the APBS biomolecular solvation software suite", Protein Sci, 27, 1: 24 August 2017, 1469-896X (Electronic) 0961-8368 (Linking), (DOI: 10.1002/pro.3280).
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49. Miao, Yinglong, McCammon, J. Andrew, Dixon, David A. (2017), "Chapter Six - Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications", Annual Reports in Computational Chemistry, Elsevier, 13: pg: 231-278, 1574-1400, (DOI: https://doi.org/10.1016/bs.arcc.2017.06.005).
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50. Klein, T., Autin, L., Kozlikova, B., Goodsell, D. S., Olson, A., Groller, M. E., Viola, I., (2017), "Instant Construction and Visualization of Crowded Biological Environments", IEEE Trans Vis Comput Graph: Aug 29, 1941-0506 (Electronic) 1077-2626 (Linking), (DOI: 10.1109/TVCG.2017.2744258).
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