2008-2009 AMS-532 Fall-Spring

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Journal Club Participants, Topics, References, and Schedule

Note: Each participant please update the Wiki as required

2008 Fall Participant Rotations or Research Group Topic References


2008.09.12 Balius, Trent Rizzo Inverse Design of ligands Altman, M. D.; et al., HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc 2008, 130, (19), 6099-113.
2008.09.19 Berger, Bill Ojima Docking and Binding mode prediction Gadakar, P. K.; et al., Pose prediction accuracy in docking studies and enrichment of actives in the active site of GSK-3beta. J Chem Inf Model 2007, 47, (4), 1446-59.
2008.00.00 Brody, Dustin Simmerling Protein Folding He, Yanan; et al., NMR structures of two designed proteins with high sequence identity but different fold and function. PNAS September 16, 2008, doi: 10.1073/pnas.0805857105.
2008.10.03 Fujimoto, Yukiji Green Continuum Electrostatic Analysis Hendsch, Z. S.; et al., Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 1994, 3, 211-226.
2008.10.10 - - - ICB&DD Symposium
2008.10.10 - - - Chemistry Research Day
2008.10.24 Goyal, Rashi Rizzo Relaxed Complex Scheme Amaro, R.E. ; Baron, R. & McCammon, J.A. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. Aided. Mol. Des. 2008, 22 (9), 693-705.
2008.00.00 Huang, Yulin Rizzo Docking Peter Kolb, Danzhi Huang, Fabian Dey, and Amedeo Caflisch. Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model. J.Med.Chem. 2008,51,1179-1188.
2008.11.07 Jiang, Tao Green G-protein Signaling Tamara L. Kinzer-Ursem ; Jennifer J. Linderman, Both Ligand- and Cel-Specific Parameters Control Ligand Agonism in a Kinetic Model of G Protein-Coupled Receptor Signaling. PLoS Comput Biol. 2007, 3 (1), 84-94.
2008.11.14 Liao, Will Zhang Deep Sequencing miRNA genes Marson, A.; et. al., Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 134(3), 521-33.
2008.00.00 McGillick, Brian Rizzo Topic Reference
2009 Spring Participant Rotations or Research Group Topic References


2009.02.06 Ray, Navamita Rotation Sugar Folding Junchao X.;et al.,Sugar Folding: A Novel Structure Prediction Tool for Oligosaccharides and Polysaccharides 1 & 2. J.Chem.Theory Comput. 2007,3,1620-1643.
2009.02.13 Wu, Jie Rotation Fingerprint of interaction Deng Z.; et. al., Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein–ligand binding interactions. J.Med.Chem. 2004,47,337–344.
2009.00.00 Au, Loretta Deng Modeling Filopodia Atilgan, E.; et al., Mechanics and dynamics of actin-driven thin membrane protrusions. Biophys J 2006, 90, 65-76.
2009.02.27 Berger, Bill Ojima Modeling FtsZ Ring Formation Condensation of FtsZ filaments can drive bacterial cell division. PNAS 2009, 106, 121-126.
2009.00.00 Brody, Dustin Rotation Topic Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science 2005, 308, 523-529.
2009.00.00 Dong, Xu Rotation Topic Reference
2009.03.20 Jiang, Tao Green G-protein Signaling Vladimir L. Katanaev; et al.,Kinetic diversity in G-protein-coupled receptor signalling. Biochem. J. 2007,401,485-495
2009.04.03 Liao, Will McCombie ChIP-seq Visel, A.; et al., ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature,2009,457, 854-859.
2009.04.17 Ray, Navamita Rizzo Crossdocking Sutherland, J.J;et al.,Lessons in Molecular Recognition.2.Assessing & Improving Crossdocking.J.Chem.Inf.Model.,2007,47,2293-2302.
2009.04.24 Wu, Jie Zhang Alternative Splicing Event Wang, E.T; et al., Alternative isoform regulation in human

tissue transcriptomes. Nature 2008, 456|27, 470-476.

2009.05.01 Au, Loretta Green G-Protein Dynamics Csercsik, D.; et al., A simple reaction kinetic model of rapid (G protein dependent) and slow (B-Arrestin dependent) transmission. J Theor Biol 2008, 255, 119-128.