Citations

Search Citations
Citations
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
BibTex | EndNote
2. 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).
BibTex | EndNote
3. 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).
BibTex | EndNote
4. 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).
BibTex | EndNote
5. 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).
BibTex | EndNote
6. 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).
BibTex | EndNote
7. 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).
BibTex | EndNote
8. 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).
BibTex | EndNote
9. 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).
BibTex | EndNote
10. 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).
BibTex | EndNote
11. 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).
BibTex | EndNote
12. 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).
BibTex | EndNote
13. 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).
BibTex | EndNote
14. 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).
BibTex | EndNote
15. 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).
BibTex | EndNote
16. 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
BibTex | EndNote
17. 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).
BibTex | EndNote
18. 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).
BibTex | EndNote
19. 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).
BibTex | EndNote
20. 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).
BibTex | EndNote
21. 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).
BibTex | EndNote
22. 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).
BibTex | EndNote
23. 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).
BibTex | EndNote
24. 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).
BibTex | EndNote
25. 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).
BibTex | EndNote
26. 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).
BibTex | EndNote
27. 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).
BibTex | EndNote
28. 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).
BibTex | EndNote
29. 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).
BibTex | EndNote
30. 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).
BibTex | EndNote
31. 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).
BibTex | EndNote
32. 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).
BibTex | EndNote
33. 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).
BibTex | EndNote
34. 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).
BibTex | EndNote
35. 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).
BibTex | EndNote
36. 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).
BibTex | EndNote
37. 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).
BibTex | EndNote
38. 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).
BibTex | EndNote
39. 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).
BibTex | EndNote
40. 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).
BibTex | EndNote
41. 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).
BibTex | EndNote
42. 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).
BibTex | EndNote
43. 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).
BibTex | EndNote
44. 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).
BibTex | EndNote
45. 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).
BibTex | EndNote
46. 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).
BibTex | EndNote
47. 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).
BibTex | EndNote
48. 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).
BibTex | EndNote
49. 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).
BibTex | EndNote
50. 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).
BibTex | EndNote
Reference Type
Author Geography
Author Affiliation

Export Multiple Citations

Check the citations that you would like to have exported.

|