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1. Singh, Alok, Nguyen, Mai H., Purawat, Shweta, Crawl, Daniel, Altintas, Ilkay, (2018), "Modular Resource Centric Learning for Workflow Performance Prediction", CoRR, 17 Apr 2018, abs/1711.0: November 15, 2017
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2. Yinglong Miao, Yu-ming M. Huang, Ross C. Walker, J. Andrew McCammon, Chia-en A. Chang, (2018), "Ligand Binding Pathways and Conformational Transitions of the HIV Protease", Biochemistry, 2018 Feb 15, 57, 9: pg: 8, 2018 Mar 6, (DOI: 10.1021/acs.biochem.7b01248).
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3. Venkatramani, Aishwarya et al., (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. Thomas E Bohl, Pek Ieong, John K Lee, Thomas Lee, Jayakanth Kankanala, Ke Shi, Özlem Demir, Kayo Kurahashi, Rommie E Amaro, Zhengqiang Wang, Hideki Aihara, (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. Rommie E. Amaro, Jerome Baudry, John Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, Jeremy C. Smith, (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. Rommie E. Amaro, Adrian J. Mulholland, (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, Yinglong, McCammon, J. Andrew, (2018), "Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor", Proceedings of the National Academy of Sciences: 03-02-2018
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9. Miao, Y., J.A. McCammon, (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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10. 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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11. Maria Carmen Mulero, Shandy Shahabi, Myung Soo Ko, Jamie M. Schiffer, De-Bin Huang, Vivien Ya-Fan Wang, Rommie E. Amaro, Tom Huxford, and Gourisankar Ghosh, (2018), "Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit", Biochemistry, 2018 May 10, 57, 20: pg: 2943-2957, 2018 May 22, (DOI: 10.1021/acs.biochem.8b00158).
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12. Kathleen Gilbert, Nickolas Forsch, Sanjeet Hegde, Charlene Mauger, Jeffrey H. Omens, James C. Perry, Beau Pontré, Avan Suinesiaputra, Alistair A. Young, Andrew D. McCulloch, (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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13. Jeffrey Wagner, Özlem Demir, Michael A Carpenter, Hideki Aihara, Daniel A Harki, Reuben S Harris, Rommie E Amaro, (2018), "Determinants of Substrate Specificity in APOBEC3B": May 4, 2018, (DOI: 10.26434/chemrxiv.6217427.v1).
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14. Huang, Y-m. M, J.A. McCammon, Y. Miao, (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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15. Fang, F., J. Huang, G. Huber, J.A. McCammon, B. Zhang., (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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16. Ahmet Erdemir, Peter J. Hunter, Gerhard A. Holzapfel, Leslie M. Loew, John Middleton, Christopher R. Jacobs, Perumal Nithiarasu, Rainlad Löhner, Guowei Wei, Beth A. Winkelstein, Victor H. Barocas, Farshid Guilak, Joy P. Ku, Jennifer L. Hicks, Scott L. Delp, Michael S. Sacks, Jeffrey A. Weiss, Gerard A. Ateshian, Steve A. Maas, Andrew D. McCulloch and Grace C. Y. Peng, (2018), "Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research", J Biomech Eng, 2017/12/17, 140, 2: pg: 11, Jan 23, 2018, 1528-8951 (Electronic) 0148-0731 (Linking), (DOI: 10.1115/1.4038768).
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17. 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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18. 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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19. 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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20. 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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21. 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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22. 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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23. 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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24. 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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25. 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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26. 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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27. 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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28. 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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29. 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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30. 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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31. 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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32. 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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33. 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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34. 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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35. 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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36. 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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37. 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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38. 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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39. 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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40. 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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41. 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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42. 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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43. 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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44. O'Dowd, B., Williams, S., Wang, H., No, J. H., Rao, G., Wang, W., McCammon, J. A., Cramer, S. P., Oldfield, E., (2017), "Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors", Chembiochem, 18, 10: pg: 914-920, May 18, 1439-7633 (Electronic) 1439-4227 (Linking), (DOI: 10.1002/cbic.201700052).
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45. P. Barros, Emília, Malmstrom, Robert D., Nourbakhsh, Kimya, Del Rio, Jason C., Kornev, Alexandr P., Taylor, Susan S., Amaro, Rommie E., (2017), "Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα", Biochemistry, February 21, 2017, 56, 10: pg: 1536-1545, 0006-2960, (DOI: 10.1021/acs.biochem.6b01152).
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46. Ou, H. D., Phan, S., Deerinck, T. J., Thor, A., Ellisman, M. H., O'Shea, C. C., (2017), "ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells", Science, 2017/07/29, 357, 6349: Jul 28, 1095-9203 (Electronic) 0036-8075 (Linking), (DOI: 10.1126/science.aag0025).
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47. Palermo, G., Ricci, C. G., Fernando, A., Basak, R., Jinek, M., Rivalta, I., Batista, V. S., McCammon, J. A., (2017), "Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9", J Am Chem Soc: Aug 07, 1520-5126 (Electronic) 0002-7863 (Linking), (DOI: 10.1021/jacs.7b05313).
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48. Palermo, Giulia, Miao, Yinglong, Walker, Ross C., Jinek, Martin, McCammon, J. Andrew, (2017), "CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations", Proceedings of the National Academy of Sciences, 114, 28: pg: 7260-7265, July 11, 2017, (DOI: 10.1073/pnas.1707645114).
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49. Pang, Y. T., Miao, Y., Wang, Y., McCammon, J. A., (2017), "Gaussian Accelerated Molecular Dynamics in NAMD", J Chem Theory Comput, 13, 1: pg: 9-19, Jan 10, 1549-9626 (Electronic) 1549-9618 (Linking), (DOI: 10.1021/acs.jctc.6b00931).
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50. Prabhu, L., Chen, L., Wei, H., Demir, O., Safa, A., Zeng, L., Amaro, R. E., O'Neil, B. H., Zhang, Z. Y., Lu, T., (2017), "Development of an AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases", Mol Biosyst, 2017/11/04, 13, 12: pg: 2509-2520, Nov 21, 1742-2051 (Electronic) 1742-2051 (Linking), (DOI: 10.1039/c7mb00391a).
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