| Yang, LeeWei, Rader, AJ, Liu, X, Jursa, CJ, Chen, SC, Karimi, HA and Bahar, I. oGNM: Online Computation of Structural Dynamics Using the Gaussian Network Model Nucleic Acids Res 34, W24-31, 2006. [JIF: 6.317] |
| Bagci, E. Z., Vodovotz, Y., Billiar,T. R., Ermentrout, G. B. and Bahar, I. Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores. Biophys J 90, 1546-1559, 2006. [JIF: 4.757] |
| Chennubhotla, C. and Bahar, I. Markov Propagation of Allosteric Effects in Biomolecular Systems Molecular Systems Biology, 2, 36, 2006. [JIF: 7.941] |
| Chennubhotla,, Chakra and Bahar, I. Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB’06, accepted. Lecture Notes in Computer Science 3909, 379-393 2006. |
| Cui, Q & Bahar, I (Eds). Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Chapman & Hall / CRC Mathematical and Computational Biology Series. CRC Press, Taylor & Francis Group, 2006. |
| Eyal, E., Yang, L. W., and Bahar, I (2006) Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22, 2619-2627. [JIF: 4.894] |
| Farkas, I. J., Wu, C., Chennubhotla, C, Bahar, I, and Oltvai, Z. N. (2006) Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics 7. Published online 2006 October 28. [JIF: 3.617] |
| Isin, B., Rader, A. J., Dhiman, H. K., Klein-Seetharaman, J., and Bahar, I. (2006) Predisposition of the dark state of rhodopsin to functional changes in structure. Proteins-Structure Function and Bioinformatics 65, 970-983. [JIF: 3.73] |
| Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar, I. An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog. 22(1):179-85, 2006. [JIF: 2.102] |
| Rader, AJ, Chennubhotla, Chakra, Yang, Lee-Wei and Bahar, Ivet. The Gaussian Network Model: Theory and Applications, in Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006. |
| Shrivastava, Indira H. and Bahar, Ivet. Common Mechanism of Pore Opening Shared by Five Different Potassium Channels. Biophys J 90, 3929-3940, 2006. [JIF: 4.757] |
| Tobi, Dror and Bahar, Ivet. Optimal Design of Protein Docking Potentials: Efficiency and Limitations. Proteins: Structure, Function, and Bioinformatics, 62, 970-981, 2006. [JIF: 3.73] |
| Belov, K., Deakin, J. E., Papenfuss, A. T., Baker, M. L., Melman, S. D., Siddle, H. V., Gouin, N., Goode, D. L., Sargeant, T. J., Robinson, M. D., Wakefield, M. J., Mahony, S., Cross, J. G. R., Benos, P. V., Samollow, P. B., Speed, T. P., Graves, J. A. M., and Miller, R. D. (2006) Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PloS Biology 4, 317-328. [JIF: 14.101] |
| Mahony, S., Benos, P. V., Smith, T. J., and Golden, A. (2006) Self-organizing neural networks to support the discovery of DNA-binding motifs Neural Networks 19, 950-962. [JIF: 2.000] |
| Camacho, C. J., Ma, H., and Champ, P. C. (2006) Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. Proteins-Structure Function and Bioinformatics 63, 868-877. [JIF: 3.73] |
| John,B., Sander,C., and Marks,D.S. 2006. Prediction of human microRNA targets. Methods in Molecular Biology. 342:101-113. |
| Arkhipov, S. N. and Maly, I. V. (2006) Contribution of whole-cell optimization via cell body rolling to polarization of T cells Physical Biology 3, 209-219. [JIF: 2.773] |
| Arkhipov, S. N. and Maly, I. V. (2006) Quantitative analysis of the role of receptor recycling in T cell polarization Biophysical Journal 91, 4306-4316. [JIF: 4.757] |
| Cheluvaraja, S. and Meirovitch, H. (2006) Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method Journal of Chemical Physics 125 024905. [JIF: 3.166] |
| Szarecka A, Meirovitch H. Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. J. Phys. Chem. B. 2006:110, 2869-2880. [JIF: 4.115] |
| White, R. P. and Meirovitch, H. (2006) Minimalist explicit solvation models for surface loops in proteins Journal of Chemical Theory and Computation 2, 1135-1151. [JIF: 3.627] |
| White, R. P. and Meirovitch, H. (2006) Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids. Journal of Chemical Physics 124 204108. [JIF: 3.166] |
| Lyman, E., Ytreberg, F.M. and Zuckerman, D. M., Resolution Exchange Simulation. Phys. Rev. Lett. 96:028105 (2006). [JIF: 7.072] |
| Lyman, E. and Zuckerman, D. M. (2006) A second look at canonical sampling of biomolecules using replica exchange simulation. Journal of Chemical Theory and Computation 2, 1200-1202. [JIF: 3.627] |
| Lyman, E. and Zuckerman, D. M., Resolution exchange simulation with incremental coarsening. J. Chem. Theory Comp. 2:656-666 (2006). [JIF: 3.627] |
| Lyman, E. and Zuckerman, D. M., Ensemble-based convergence analysis of biomolecular trajectories. Biophysical J., 91:164-172 (2006). [JIF: 4.757] |
| Ytreberg, F.M., Swendsen, R.H. and Zuckerman, D.M. (2006) Comparison of free energy methods for molecular systems. J. Chem. Phys 125, 184114. [JIF:3.166 ] |
| Ytreberg, F.M. and Zuckerman, D.M. (2006) BlackBox Reweighting. arXiv:physics/0609194v1 [physics.comp-ph]. |
| Ytreberg, F. M. and Zuckerman, D. M. Simple estimation of absolute free energies for biomolecules, J. Chem. Phys. 124:104015 (2006). [JIF: 3.166] |
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