2005 Publications

Bahar, Ivet & Rader, AJ. (2005) “Coarse-grained normal mode analysis in structural biology.” Current Opinion in Structural Biology 15:1-7. [JIF: 11.215]

Tobi, Dror & Bahar, Ivet. (2005) “Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State” Proc Natl Acad Sci (USA) 102, 18908-18913. [JIF: 9.643]

Berberich, Jason, Yang, Lee Wei, Bahar, Ivet & Russell, Alan J (2005) “Analysis of the impact of silver ions on creatine amidinohydrolase.” ACTA Biomaterialia 1(2) pg.183-191. [JIF: 2.132]

Berberich, Jason, Yang, Lee Wei, Madura, Jeff, Bahar, Ivet & Russell, Alan J. (2005) “A Stable Three Enzyme Creatinine Biosensor Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase.” ACTA Biomaterialia 1(2) pg.173-181. [JIF: 2.132]

Chennubhotla, Chakra, Rader, AJ, Yang, Lee-Wei & Bahar, Ivet. (2005) “Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies” Physical Biology 2, S173-S180. [JIF: 2.773]

Rader, AJ, Vlad, Daniel & Bahar, Ivet (2005) “Maturation Dynamics of Bacteriophage HK97 Capsid” Structure (Camb) 13:413-21. [JIF: 5.738]

Ramaswamy, Amutha, Bahar, Ivet & Ioshikhes, Ilya (2005) “Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants” Proteins: Structure, Function and Bioinformatics 58:683-696. [JIF: 3.73]

Yang, Lee Wei & Bahar, Ivet. (2005) “Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes.” Structure 13: 893-904. [JIF: 5.738]

Yang, Lee Wei, Liu, Xiong, Jursa, Christopher Jon, Holliman, Mark, Rader, A.J., Karimi, Hassan & Bahar, Ivet. (2005) “iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model.” Bioinformatics 21: 2978 – 2987. [JIF: 4.894]

Alexander, A.M., Pecoraro, C., Styche, A., Rudert, W.A., Benos, P.V., Ringquist, S., Trucco, M. (2005) SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing,” Biotechniques38:87-94. [JIF: 2.462]

Corcoran, D.L., Feingold, E., Dominick, J., Wright, M., Harnaha, J., Trucco, M., Giannoukakis, N., Benos, P.V. (2005) “FOOTER: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements,” Genome Res.15:840-847. [JIF: 10.256]

Corcoran, D.L., Feingold, E., Benos, P.V. (2005) “FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting,” Nucl Acids Res. (2005) 33:W442-446. [JIF: 6.317]

Mahony, S., Golden, A., Smith, T.J., Benos, P.V. (2005) “Improved detection of DNA motifs using a self-organized clustering of familial binding profiles,” Intelligent Systems in Molecular Biology, Bioinformatics, 21 (Suppl 1):i283-i291. (Approval conference publication rate for ISMB: 13%) [JIF: 4.894]

Ringquist, S., Pecoraro, C., Gilchrist, C., Styche, A., Rudert, W., Benos, P.V., Trucco, M. (2005) “SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms,” Nucl Acids Res.33:W548-552. [JIF: 6.317]

Rogulski, K.R., Cohen, D.E., Corcoran, D.L., Benos, P.V., Prochownik, E.V. (2005) “Deregulation of common genes by c-Myc and its direct target, MT-MC1,” Proc Natl Acad Sci USA 102:18968-18973. [JIF: 9.643]

Workman, C.T., Yin, Y., Corcoran, D.L., Ideker, T., Stormo, G.D., Benos, P.V. “enoLOGOS: a versatile web tool for energy normalized sequence logos,” Nucl Acids Res.33:W389-392. [JIF: 6.317]

Camacho CJ. (2005) Modeling side chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins. 2005 60, 245-251. [JIF: 3.73]

Camacho CJ, Zhang C (2005) FastContact: rapid estimate of contact and binding free energies, Bioinformatics 2005; 21: 2534-2536. [JIF: 4.894]

Comeau SR, Camacho CJ (2005) Predicting oligomeric assemblies: N-mers a primer, J. Struct. Biol. 2005; 150: 233-244. [JIF: 3.496]

Comeau S, Vajda S, Camacho CJ. (2005) Performance of the first protein docking server ClusPro in CAPRI rounds3-5. Proteins. 2005 60, 239-244. [JIF: 3.73]

Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. (2005) Optimal clustering for detecting near native conformations in protein docking. Biophys. J. 2005 89, 867-875. [JIF: 4.757]

Chen, P. Y., Manninga, H., Slanchev, K., Chien, M., Russo, J. J., Ju, J., Sheridan, R., John, B., Marks, D. S., Gaidatzis, D., Sander, C., Zavolan, M. & Tuschl, T. (2005). The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19, 1288-93. [JIF: 15.05]

Topf, M., Baker, M. L., John, B., Chiu, W. & Sali, A. (2005). Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 149, 191-203. [JIF: 3.496]

Cheluvaraja S, Meirovitch H. (2005) Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo Method: Application to peptides. J. Chem. Phys. 2005:122, 054903-1 – 054903-14. 10904. [JIF: 3.166]

Cheluvaraja S, Meirovitch H. (2005) Calculation of the entropy and free energy from Monte Carlo simulations of a peptide stretched by an external force. J. Phys. Chem. B. 109, 21963-21970. [JIF: 4.115]

White RP, Funt J, Meirovitch H. (2005) Calculation of the entropy of lattice polymer models from Monte Carlo trajectories. Chem. Phys. Lett. 410, 430-435. [JIF: 2.462]

White RP, Meirovitch H. (2005) Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo Method. J. Chem. Phys. 123, 214908-11. [JIF: 3.166]

Ytreberg, F. M. and Zuckerman, D. M. (2005) Peptide Conformational equilibria computed via a single-stage shifting protocol, J. Phys. Chem. B., 109:9096-9103. [JIF: 4.115]