2008-2009 AMS-532 Fall-Spring

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.