| Bahar I, Chennubhotla, C. and Tobi, D. (2007)Intrinsic Enzyme Motions in the Unbound State and Relation to Allosteric Regulation. Current Opinion Structural Biology, 17 (in press). [JIF: 11.215] |
| Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. (2007) Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure. 15, 741-9. [JIF: 5.738] |
| Eyal, E., Chennubhotla, C., Yang, L. W., and Bahar I. (2007) Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models. Bioinformatics 22, 2619-27. [JIF: 4.894] |
| Eyal E, Pietrokovski S, Bahar I (2007) Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. Bioinformatics 23, 1837-9. [JIF: 4.894] |
| Bahar I, Chennubhotla, CReply to comment on elastic network models and proteins. Physical Biology 4, 64-65. [Journal Impact Factor, JIF: 2.773] |
| Chennubhotla C. and Bahar I (2007) Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Computational Biology, accepted. [JIF: 4.914] |
| Chennubhotla C. and Bahar I . (2007) Markov methods for hierarchical coarse-graining of large protein dynamics. J Comput Biol.14, 765-76. [JIF: 2.000] |
| Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. (2007) Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity. J Cell Physiol. 211, 748-58. [JIF: 3.638] |
| Lazo, J.S., Skoko, J.J., Werner, S., Mitasev, B., Bakan, A., Koizumi, F, Yellow-Duke, A., Bahar I, Brummond, K.M. (2007) Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library. J Pharmacol Exp Ther. 322 940-7. [JIF: 3.956] |
| Tobi D, Bahar I. (2007) Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? BMC Bioinformatics 8, 226. [JIF: 3.617] |
| Vries, J. K., Liu, X., and Bahar I. (2007) Relationship between n-gram patterns and secondary structure. Proteins-Structure Function and Bioinformatics 68, 830-838. [JIF: 3.730] |
| Benos P. V., Corcoran, D. L., and Feingold, E. (2007). Footer: Web-Based Identification of Evolutionary Conserved DNA cis-regulatory Elements. Methods in Molecular Biology/Comparative Genomics, edited by N. Bergman, Totowa, New Jersey: Humana Press, Inc. |
| Feng, H., Taylor, J.L., Benos P.V., Newton, R., Downing, R., Waddell, K., Chang, Y., Moore, P.S, (2007) Subtraction of the human transcriptome to search for human tumor viruses. J Virol (in print). [JIF: 5.341] |
| Lu, Y., Mahony, S., Benos P.V., Rosenfeld, R., Simon, I., Breeden, L., Bar-Joseph, Z. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol. 8, R146. [JIF: 7.172] |
| Mahony, S. and Benos P.V. (2007) STAMP; a web tool for exploring DNA-binding motif similarities. Nucleic Acids Research. [JIF: 6.317] |
| Mahony, S., Corcoran, D. L., Feingold, E., and Benos P.V. (2007) Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome. Genome Biology. [JIF: 7.172] |
| Mahony, S., Auron, P. E., and Benos P.V. (2007) DNA Familial binding profiles made easy: Comparison of various motif alignment and clustering strategies. PloS Comput Biology 3, e61. [JIF: 4.914] |
| Mahony, S., Auron, P.E., Benos P.V. (2007) Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics 23, i297-i304. [JIF: 4.894] |
| Mikkelsen, T.S. and et al. [Benos, P.V.] (2007) Genome of the marsupial Monodelphia domestica reveals innovation in on-coding sequences. Nature 447, 167-177. [JIF: 26.681] |
| Ringquist, S., Pecoraro, C., Lu, Y., Styche, A., Rudert, W. A., Benos, P.V., and Trucco, M. (2007). Web-based primer design software for genome scale SNP mapping by pyrosequencing. Humana Press, Inc., Totowa, New Jersey. |
| Bueno, M and Camacho CJ (2007) Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI. Proteins, in press. [JIF: 3.730] |
| Bueno M, Camacho CJ, Sancho J. (2007) SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles. Proteins 68, 850-62. [JIF: 3.730] |
| Camacho CJ et al. (2007) “A Novel Murine Model of the Anti-synthetase Syndrome Induced by Immunization with Histidyl-tRNA Synthetase: Critical Role of Species-specific Epitopes in Self-directed B and T Cell Responses” accepted. |
| Champ PC, Camacho CJ (2007) FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Res. 35 (Web Server issue), W556-60. Epub 2007 May 30. [JIF: 6.317] |
| Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. (2007) Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity. J Cell Physiol. 211, 748-58. [JIF: 3.638] |
| Prasad, J. C., Goldstone, J. V., Camacho CJ, Vajda, S., and Stegeman, J. J. (2007) Ensemble modeling of substrate binding to cytochromes p450: Analysis of catalytic differences between CYP1A orthologs. Biochemistry 46, 2640-2654. [JIF: 3.633] |
| Lee, J., Li, Z., Brower-Sinning, R., John, B. (2007) Regulatory circuit of human microRNA biogenesis. PLoS Comput Biol. [JIF: 4.914] |
| Arkhipov, S.N. and Maly, I.V. (2007) A model for the interplay of receptor recycling and receptor-mediated contact in T cells. PLoS ONE, 2, e633. |
| Grigoriev, I. , Splinter, D., Keijzer, N., Wulf, P.S., Demmers, J., Ohtsuka, T., Modesti, M., Maly, I.V., Grosveld, F., Hoogenraad, C.C., and Akhmanova, A.. (2007) Rab6 regulates transport and targeting of exocytotic carriers. Dev. Cell, 13, 305–314. [JIF: 13.523] |
| Meirovitch H. (2007) Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Curr Opin Struct Biol. 17, 181-6. [JIF: 11.215] |
| Vries, J. K., Liu, X., and Bahar, I. (2007) Relationship between n-gram patterns and secondary structure. Proteins-Structure Function and Bioinformatics 68, 830-838. [JIF: 3.73] |
| Lyman, E. and Zuckerman, D.M. (2007) Annealed importance sampling of peptides. J. Chem. Phys., in press. [JIF: 3.166] |
| Lyman, E. and Zuckerman, D.M. (2007) On the convergence of biomolecular simulations: Determining the effective sample size. J. Phys. Chem. B, in press. [JIF: 4.115] |
| Ytreberg, F.M., Aroutiounian, S.Kh., and Zuckerman, D.M. (2007) Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model. J. Chem. Theory Comp., in press; Web Release Date: August 25, 2007. [JIF: 3.627] |
| Zhang, Bin W., Jasnow, David, and Zuckerman, Daniel M. (2007) Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin. Proc Natl Acad Sci (USA), in press. |
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