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Institute Publications 2005

 

Andrec, M., B.N. Kholodenko, R.M. Levy, E. Sontag.

"Inference of signaling and gene regulatory networks by steady-state perturbation experiments: Structure and accuracy." J Theor Biol. 232:427-441 (2005)

 

Andrec, M., A.K. Felts, E. Gallicchio, R.M. Levy.

"Protein folding pathways from replica exchange simulations and a kinetic network model." Proc Natl Acad Sci USA. 102:6801-6806 (2005)

 

Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts, T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky, L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, R.M. Levy.

"Integrated Modeling Program, Applied Chemical Theory (IMPACT)." J Comp Chem. 26:1752-1780 (2005)

 

Bar-Nahum, G., V. Epshtein, A. Ruckenstein, R. Rafikov, A. Mustaev, E. Nudler.

"A ratchet mechanism of transcription elongation and its control." Cell. 120:183-193 (2005)

 

Berman, H.M., L.F. Ten Eyck, D.S. Goodsell, N.M. Haste, A. Kornev, S. Taylor.

"The cAMP binding domain: An ancient signaling module." Proc Natl Acad Sci USA. 102:45-50 (2005)

 

Chaves, M., R. Albert, E.D. Sontag.

"Robustness and fragility of Boolean models for genetic regulatory networks." J Theor Biol. 235:431-439 (2005)

 

Das, K., P.J. Lewi, S.H. Hughes, E. Arnold.

"Crystallography and the design of anti-AIDS drugs: conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors." Prog Biophys Mol Biol. 88:209-231 (2005)

 

De Leenheer, P., D. Angeli, E.D. Sontag.

"On predator-prey systems and small-gain theorems." J. Mathematical Biosciences and Engineering. 2:25-42 (2005)

 

Dutta, S., H.M. Berman.

"Large macromolecular complexes in the Protein Data Bank: A status report." Structure. 13:381-388 (2005)

 

Ge, W., B. Schneider, W.K. Olson.

"Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids." Biophys J. 2:1166-1190 (2005)

 

Huang, Y.J., R. Powers, G.T. Montelione.

"Protein NMR Recall, Precision, and F-measure scores (RPF Scores): Structure quality assessment measures based on information retrieval statistics." J Amer Chem Soc. 127:1665-1674 (2005)

 

Kapanidis A.N., E. Margeat, T.A. Laurence, S. Doose, S.O. Ho, J. Mukhopadhyay, E. Kortkhonjia, V. Mekler, R.H. Ebright, S. Weiss.

“Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis.” Mol Cell. 20:347-356 (2005)

 

Knight, J.L., V. Mekler, J. Mukhopadhyay, R.H. Ebright, R.M. Levy.

"Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: Developing benchmarks of model quality and reliability." Biophys J. 88:925-938 (2005)

 

Lee, N.K., A.N. Kapanidis, Y. Wang, X. Michalet, J. Mukhopadhyay, R.H. Ebright, S.Weiss.

"Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation." Biophys J. 88:2939-2953 (2005)

 

Li, Y., S. Kim, B. Brodsky, J. Baum.

"Identification of Partially Disordered Peptide Intermediates through Residue-Specific NMR Diffusion Measurements." J Amer Chem Soc. 127:10490-10491 (2005)

 

Liu, G., A.M. Geurts, K. Yae, A.R. Srinivasan, S.C. Fahrenkrug, D.A. Largaespada, J. Takeda, K. Horie, W.K. Olson, P.B. Hackett.

"Target-site Preferences of Sleeping Beauty Transposons." J Mol Biol. 346:161-173 (2005)

 

Liu, G., Y. Shen, H.S. Atreya, D. Parish, Y. Shao, D.K. Sukumaran, R. Xiao, A. Yee, T.B. Acton, C.H. Arrowsmith, G.T. Montelione, T. Szyperski.

"NMR data collection and analysis protocol for high-throughput protein structure determination." Proc Natl Acad Sci USA. 102:10487-10492 (2005)

 

Matsumoto, A., I. Tobias, W.K. Olson.

"Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 1. Comparison of Computed Motions with the Predicted Behavior of an Ideal Elastic Rod." J Chem Theory Comput. 1:117-129 (2005)

 

Matsumoto, A., I. Tobias, W.K. Olson.

"Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule." J Chem Theory Comput.  1:130-142 (2005)

 

Nickels, B.E., S.J. Garrity, V. Mekler, L. Minakhin, K. Severinov, R.H. Ebright, A. Hochschild.

"The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation." Proc Natl Acad Sci U S A. 102:4488-4493 (2005)

 

O'Flanagan, R.A., G. Paillard, R. Lavery, A.M. Sengupta.

"Non-additivity in protein-DNA binding." Bioinformatics. 21:2254-2263 (2005)

 

Ravindranathan, K.P., E. Gallicchio, R.M. Levy.

"Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose Binding Protein." J Mol Biol. 353:196-210 (2005)

 

Revyakin, A., R.H. Ebright, T.R. Strick.

"Single-molecule DNA nanomanipulation: Improved resolution through use of shorter DNA fragments." Nature Methods. 2:127-138 (2005)

 

Robins, H., Y. Li, R.W. Padgett.

"Predicting microRNA Targets with High Precision." Proc. Natl. Acad. Sci. USA. 102:4006-4009 (2005)

 

Roma, D.M., R.A. O'Flanagan, A.E. Ruckenstein, A.M. Sengupta, R. Mukhopadhyay.

"Optimal path to epigenetic switching." Physical Review E. 71:011902 (2005)

 

Sontag, L., D.E. Axelrod.

"Evaluation of pathways for progression of heterogeneous breast tumors." J Theor. Biol. 232:179-189 (2005)

 

Traulson, A., A. Sengupta, M. Nowak.

"Stochastic Evolutionary Dynamics at Two Levels." J Theor. Biol.

 

Tuske S., S.G. Sarafianos , X. Wang, B. Hudson, E. Sineva, J. Mukhopadhyay, J.J. Birktoft, O. Leroy, S. Ismail, A.D. Clark Jr, C. Dharia, A. Napoli, O. Laptenko, J. Lee, S. Borukhov, R.H. Ebright, E. Arnold.

"Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation." Cell 122:541-552 (2005)

 

Westbrook, J., N. Ito, H. Nakamura, K. Henrick, H.M. Berman.

“PDBML: the representation of archival macromolecular structure data in XML.” Bioinformatics. 21:988-992 (2005)

 
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