2008-2009 AMS-532 Fall-Spring
From Rizzo_Lab
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. |