The Jernigan Laboratory - Personnel: Sen

Research Interests

Elastic network modeling of proteins and nucleic acids to elucidate structure-function relationships
Development and improvement of secondary and tertiary structure prediction methods
Application of artificial intelligence to protein-protein binding site predictions
Topological and functional interpretations of protein-protein interaction networks
Modeling mechanical behaviors of polymer nanocomposites

Publications

Journal Articles (refereed)

1) Sen, T. Z., Bahar, I., Erman, B., Lauprêtre, F., Monnerie, L., "Local chain dynamics of cis-1,4-polybutadiene and cis-1,4-polyisoprene. A comparative study based on Cooperative Kinematics theory and NMR experiments", Macromolecules, 32, 3017-3024, 1999.

2) Konuklar, F. A. S., Aviyente, V., Sen, T.Z., Bahar, I., "Modeling the deamidation of asparagine residues via succinimide intermediates", Journal of Molecular Modeling, 7(5), 147-160, 2001.

3) Valladares, D., Toki, S., Sen, T.Z., Yalcin, B., Cakmak, M, “Real time birefringence, true stress and true strain behavior of natural rubber: Effect of crosslink density”, Macromolecular Symposia, 185, 149-166, 2002.

4) Kloczkowski, A., Sen,T.Z., Jernigan, R.L., “The transfer matrix method for lattice proteins-an application with cooperative interactions”, Polymer, 45, 707-716, 2004.

5) Varshney, V., Dirama, T.E., Sen, T.Z., Carri, G.A., “A Minimal Model for the Helix-Coil Transition of Worm-like Polymers. Insights from Monte Carlo Simulations and Theoretical Implications”, Macromolecules, 37, 8794-8804, 2004.

6) Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K.-M., Wang, C.-Z., Ihm, Y., Cao, H., Gu, X, Dobbs, D., “Predicting binding sites of hydrolase-inhibitor complexes by combining several methods”, BMC Bioinformatics, 5:205, 2004.

7) Cheng, H., Sen, T.Z., Kloczkowski, A., Margaritis, D., Jernigan, R.L., “Prediction of protein secondary structure by mining fragments database”, Polymer, 46, 4314-4321, 2005.

8) Kloczkowski, A., Sen, T.Z., Sharaf, M.A., “The largest eigenvalue method for stereo-regular vinyl chains”, Polymer, 46, 4373-4383, 2005.

9) Sen, T.Z., Jernigan, R.L., Garnier, J., Kloczkowski, A., “The GOR V server for protein secondary structure assignment”, Bioinformatics, 21(11), 2787-2788, 2005.

10) Fernandez, A., Tawfik, D.S., Berkhout, B., Sanders, R., Kloczkowski, A., Sen, T.Z., Jernigan, R..L., “Protein Promiscuity: Drug Resistance and Native Functions -- HIV-1 Case.”, J. Biomol. Struct. Dyn., 22(6), 615-624, 2005.

11) Sen, T.Z., Sharaf, M.A., Mark, J.E., Kloczkowski, A., “Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers”, Polymer, 46(18), 7301-7308, 2005.

12) Mark, J.E, Abou-Hussein, R., Sen, T.Z., Kloczkowski, A., Sharaf, M.A., “Some simulations on filler reinforcement in elastomers”, Polymer, 46(21), 8894-8904, 2005.

13) Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I., Mark, J.E., “Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments”, European Polymer Journal, in press.

14) Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I., Mark, J.E., “Molecular Modeling of Matrix Chain Deformation in Nanofiber Filled Composites”, Colloid & Polymer Science, in press.

15) Sen, T.Z., Feng, YP, Garcia, J.V., Kloczkowski, A., Jernigan, R.L., “The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models”, Journal of Chemical Theory and Computation, 2(3), 696-704, 2006.

16) Sen, T.Z., Kloczkowski, A., Jernigan, R.L., “Functional clustering of yeast proteins from the protein-protein interaction network”, BMC Bioinformatics, 7(355), 2006.

17) Sen, T.Z., Kloczkowski, A., Jernigan, R.L., “A DNA-centric look at protein-DNA complexes”, Structure, 14(9), 1341-1342, 2006.

18) Sen, T.Z., Cheng, H.T., Kloczkowski, A., Jernigan, R.L., “A consensus data mining secondary structure prediction by combining GOR V and fragment database mining ”, Protein Science, 15(11), 2499-2506, 2006.

Book Chapters (refereed)

1) Sen, T.Z., Jernigan, R.L. “Optimizing cutoff distances and spring constants for the Gaussian network model of ATP-binding proteins”, in “Normal mode analysis: theory and applications to biological and chemical systems”, Eds Q. Cui, I. Bahar, 2005.

2) Kloczkowski, A., Sen, T.Z. “Magnetic, piezoelectric, pyroelectric, and ferroelectric properties of synthetic and biological polymers”, in “Physical properties of polymers handbook”, Ed. James E. Mark, 2nd edition, Springer-Verlag, in press.

Conference Proceedings (refereed)

1) Sen, T. Z., Toki, S., Cakmak, M., “Real time development of stress and birefringence in PET during uniaxial stretching as detected by spectral birefringence technique”, Annual Technical Conference- Society of Plastics Engineers (ANTEC), 59(2), 1510-1514, 2001.

2) Toki, S., Valladares, D., Sen, T.Z., Cakmak, M., “Real time birefringence development of orientation in polymers during uniaxial stretching as detected by robust spectral birefringence technique.”, Annual Technical Conference – Society of Plastics Engineers (ANTEC), 59(2), 1830-1834, 2001.

3) Koike, Y., Sen, T.Z., Cakmak, M., “Real time development of orientation in PP during stretching as detected by spectral birefringence technique”, Annual Technical Conference – Society of Plastics Engineers (ANTEC), 60(2), 1550-1555, 2002.

4) Mulligan, J., Cakmak, M., Sen, T.Z., “Basic mechanisms of structural ordering in uniaxial stretching of PLA using fully automated on-line birefringence coupled with true stress-true strain measurement”, Annual Technical Conference - Society of Plastics Engineers (ANTEC), 60(2), 1646-1650, 2002.