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Balasubramanian, S., F. Xu, W.K. Olson. Chen, K., J. Maaskola, M. L. Siegal, N. Rajewsky. "Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study." PLoS ONE 4(5):e5681 (2009) Costa, I.G., A. Schönhuth, C. Hafemeister, A. Schliep. "Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series." Bioinformatics 25(12):i6-i14 (2009) Cramer, T., T. Steinbrecher, T. Koslowski, D.A. Case, F. Biscarini, F. Zerbetto. Frenkel, Y.V., E. Gallicchio, K. Das, R.M. Levy, E. Arnold. "Molecular Dynamics Study of Non-nucleoside HIV-1 RT Inhibitor TMC278/Rilpivirine Aggregates: Correlation between Amphiphilic Properties of the Drug and Oral Bioavailability." J. Med. Chem. 52:5896-5905 (2009) Fuller, A.A., D. Du, F. Liu, J.E. Davoren, G. Bhabha, G. Kroon,D.A. Case, H.J. Dyson, E.T. Powers, P. Wipf, M. Gruebele,J.W. Kelly. Gallicchio, E., K. Paris, R.M. Levy. "The AGBNP2 Implicit Solvent Model." J. Chem. Theory Comput. 5(9):2544-2564 (2009) Georgi, B., J. Schultz, A. Schliep. "Partially-supervised protein subclass discovery with simultaneous annotation of functional residues." BMC Struct. Biol. 9:68 PMID:19857261 (2009) Haq, O., R.M. Levy, A.V. Morozov, M. Andrec. "Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease." BMC Bioinformatics 10(Suppl 8):S10 (2009) Hou, T., Z. Xu, W. Zhang, W. McLaughlin, D.A. Case, Y. Xu, W. Wang. "Characterization of domain-peptide interaction interface: a unified model to decipher the binding specificity of SH3 domains." Mol. Cell. Proteomics 8:639-649 (2009) Lang, P.T., S.R. Brozell, S. Mukherjee, E.F. Pettersen, E.C. Meng, V. Thomas, R.C. Rizzo, D.A. Case, T.L. James, I.D. Kuntz. Lapelosa, M., E. Gallicchio, G. Ferstandig Arnold, E. Arnold, R.M. Levy. "In silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes." J. Mol. Biol., 385, 675-691 (2009) Liu, J., W.H. Miller, F. Paesani, W. Zhang, D.A. Case. "Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum." J. Chem. Phys. 131:164509 (2009) Morozov, A.V., K. Fortney, D.A. Gaykalova, V.M. Studitsky, J. Widom, E.D. Siggia. Noodleman, L., D.A. Case. "Broken symmetry states of iron–sulfur clusters." Encyclopedia of Inorganic Chemistry,Second Edition, R.H. Crabtree, ed. New York, Wiley & Sons (2009) Olson, W.K., A.V. Colasanti, L. Czapla, G.H. Zheng. “Insights into the Sequence-dependent Macromolecular Properties of DNA from Base-pair Level Modeling,” in Coarse-Graining of Condensed Phase and Biomolecular Systems, Gregory A. Voth, Ed., CRC Press, Taylor and Francis Group, Boca Raton, FL, pp. 205-223 (2009). Olson, Wilma K., Esguerra, Mauricio, Xin, Yurong, and Lu, Xiang-Jun “New Information Content in RNA Base Pairing Deduced from Quantitative Analysis of High-resolution Structures,” Methods 47(3):117-186 (2009) Olson, W.K., A.R. Srinivasan, A.V. Colasanti, G.H. Zheng, D. Swigon. “DNA Biomechanics” Handbook of Molecular Biophysics: Methods and Applications, Henrik G. Bohr, Ed., WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, 359-382 (2009).
Paris, K.A., O. Haq, A.K. Felts, K. Das, E. Arnold, R.M. Levy. "Conformational Landscape of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Non-Nucleoside Inhibitor Binding Pocket: Lessons for Inhibitor Design from a Cluster Analysis of Many Crystal Structures." J. Med. Chem. 52:6413-6420 (2009) Wong, V., D.A. Case and A. Szabo. Wu, K-P, D.S. Weinstock, C. Narayanan, R.M. Levy, J. Baum. "Structural reorganization of a-synuclein at low pH observed by NMR and REMD simulations." J. Mol. Biol. 391: 784-796 (2009) Xin, Y., W.K. Olson. “BPS: A Database of RNA Base-pair Structures,” Nucleic Acids Res. 37:D83-D88 (2009). Zawadzki, K.A., A.V. Morozov, J.R. Broach. "Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae." Mol. Biol. Cell 20:3503-3513 (2009) Zheng, G.H., X.J. Lu, W.K. Olson. “Web 3DNA – A Web Server for the Analysis, Reconstruction, and Visualization of Three-dimensional Nucleic-acid Structures.” Nucleic Acids Res. 37:W240-W246 (2009) Zheng, W., M. Andrec, E. Gallicchio, R.M. Levy. "Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics." J. Phys. Chem. B 113:11702-11709 (2009)
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