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About

This project was organized through the NSF-funded fellowship project, SCALE-IT, as a interdisciplinary team-oriented project.

Below is a table of people who have worked on this project:

Name Department Webpage
David D. Jenkins Electrial Engineering and Computer Science [LINK]
Jason B. Harris Genome Science and Technology [LINK]
Stephanie Rickett Electrial Engineering and Computer Science [LINK]
Jordan M. Utley Genome Science and Technology [LINK]
Jonathan Reyles Genome Science and Technology [LINK]
Elizabeth Howell Biochemistry and Cellular and Molecular Biology [LINK]
Jerome Baudry Biochemistry and Cellular and Molecular Biology [LINK]
Robert J. Hinde Chemistry [LINK]

If you have any problems/questions, email: jbaudry [at] utk [dot] edu


If you use this service, please cite the following papers:

  1. STAAR: Statistical analysis of aromatic rings. Jenkins, D. D., Harris, J. B., Howell, E. E., Hinde, R. J. and Baudry, J. J. Comput. Chem.. 2012 [LINK]
  2. A Preference for Edgewise Interactions between Aromatic Rings and Carboxylate Anions:  The Biological Relevance of Anion−Quadrupole Interactions. Jackson, M. R., Beahm, R., Duvvuru, S., Narasimhan, C., Wu, J., Wang, H. N., Philip, V. M., Hinde, R. J., and Howell, E. E. The Journal of Physical Chemistry B 2007 111 (28), 8242-8249. [LINK]
  3. A Survey of Aspartate−Phenylalanine and Glutamate−Phenylalanine Interactions in the Protein Data Bank: Searching for Anion−π Pairs. Philip, V., Harris, J., Adams, R., Nguyen, D., Spiers, J, Baudry, J., Howell, E. E., Hinde, R. J. Biochemistry 2011 50 (14), 2939-2950. [LINK]


Papers that have cited this work:

  1. Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). Garcia-Perez, J., Rueda, P., Alcami, J., Rognan, D., Arenzana-Seisdedos, F., Lagane, B., Kellenberger, E., (2011) The Journal of Biological Chemistry, vol. 286 (38) p. 33409-21.
  2. Thermodynamics of stacking interactions in proteins. Procacci, P., (2011) Annual Reports Section "C" (Physical Chemistry), vol. 107, p. 242.
  3. Aromatic rings in chemical and biological recognition: energetics and structures. Salonen, L. M., Ellermann, M., and Diederich, F., (2011) Angewandte Chemie (International ed. in English), vol. 50, no. 21, pp. 4808-42.
  4. The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction. Meenan, N.A.G., Sharma, A., Fleishman, S.J., MacDonald, C.J., Morell, B., Boetzel, R., Moore, G. R., Baker, D. and Kleanthous, C. (2010) Proceedings of the National Academy of Sciences, 107(22), 10080-10085
  5. DevS Oxy Complex Stability Identifies This Heme Protein as a Gas Sensor in Mycobacterium Tuberculosis Dormancy. Ioanoviciu, A., Meharenna, Y. T.; Poulos, T. L., and Ortiz de Montellano, P. R. (2009) Biochemistry, 48(25), 5839-5848.
  6. Experimental evidence for interactions between anions and electron-deficient aromatic rings. Berryman, O. B. and Johnson, D. W., Chemical Communications ( Cambridge, United Kingdom) (2009), (22), 3143-3153.
  7. Binding Mechanisms in Supramolecular Complexes. Schneider, H. J. Angewandte Chemie, International Edition (2009), 48(22), 3924-3977.
  8. Extension of the Tryptophan x2,1 Dihedral Angle-W3 Band Frequency Relationship to a Full Rotation: Correlations and Caveats. Juszczak, L. J. and Desamero, R. Z. B. Biochemistry (2009), 48(12), 2777-2787.
  9. Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate. Dharmarajan, L., Case, C. L., Dunten, P., and Mukhopadhyay, B. FEBS Journal (2008), 275(23), 5810-5819.
  10. Explaining an Unusually Fast Parasitic Enzyme: Folate Tail-Binding Residues Dictate Substrate Positioning and Catalysis in Cryptosporidium hominis Thymidylate Synthase. Martucci, W. E., Vargo, M. A., and Anderson, K. S. Biochemistry (2008), 47(34), 8902-8911.
  11. Thermodynamics of stacking interactions in proteins. Marsili, S., Chelli, R., Schettino, V., and Procacci, P., Physical Chemistry Chemical Physics (2008),10(19),2673-2685.