2008-2009 AMS-532 Fall-Spring

From Rizzo_Lab
Jump to: navigation, search

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

NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT

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

NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT

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.