2007-2008 AMS-532 Fall-Spring
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Journal Club Participants, Topics, References, and Schedule
Note: Each participant please update the Wiki as required
2007 Fall | Participant | Rotations or Research Group | Topic | References
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
2007.09.21 | Patsalo, Vadim | Green Group | structural inter. networks | Kim, P.M. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 2006, 314, 1938-41. |
2007.09.28 | Barsegian, Garen | Deng, Rizzo, Simmerling | dynamic positional info. | Jaeger, J.; Reinitz, J. On the dynamic nature of positional information. Bioessays 2006, 28, 1102-11. |
2007.10.12 | Goyal, Rashi | Rizzo Group | avian influenza | Russell, R.J. et al. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 2006, 443, 45-49.
Amaro, R.E. et al. Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design. JACS 2007, 129, 7764-65. |
2007.10.26 | Jiang, Tao | Zhu, Green | mass spec feature extract | Wang, X. et al. Feature extraction in the analysis of proteomic mass spectra. Proteomics 2006, 6, 2095-100. |
2007.11.02 | Han, Ji | Green Group | allosteric comm | Suel, G.M. et al. Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nature Structural Biology 2003, 10, 59-69. |
2007.11.16 | Mukherjee, Sudipto | Rizzo Group | virtual ligand screening | Klebe, G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discovery Today 2006, 11, 580-94. |
2007.11.30 | McGillick, Brian | Rizzo Group | viral entry | Cardozo, T. et al. Structural basis for coreceptor selectivity by the HIV type 1 V3 loop. Aids Research and Human Retroviruses 2007, 23, 415-26. |
2007-2008 | Shou-Chiang, Peng | Green Rizzo | cheminformatics | Ertl, P. et al. Natural product-likeness score and its applications for prioritization of compound libraries. JCIM 2008, 48, 68-74. |
2008 Spring | Participant | Rotations or Research Group | Topic | References
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
2008.02.08 | Rao, Abhishek | Green, Fortmann, Rizzo | cation transport | Kang, Y. and Fortmann, C.M. A structural basis for the Hodgkin and Huxley relation. Applied Physics Letters 2007, 91, 223903-3. |
2008.03.07 | Barsegian, Garen | Deng, Rizzo, Simmerling | anti-cancer drug design | Blagg, J. et al. Potent pyrimidinetrione-based inhibitors of MMP-13 with enhanced selectivity over MMP-14. ELSEVIER 2005, 15, 1807-1810 |
2008.03.14 | Huang, Yulin | Simmerling, Rizzo, Green | Docking | Niu, C.; Yin, J.; Zhang, J.; Vederas, J. C.; James, M. N., Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro. Bioorg Med Chem 2008, 16, (1), 293-302. |
2008.03.28 | Balius, Trent | Rizzo Group | drug design | Liu, B.; Bernard, B.; Wu, J. H., Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations. Proteins 2006, 65, (2), 331-46 |
2008.04.04 | Goyal, Rashi | Rizzo Group | drug design | Landon, M.R.; Amaro, R.E.; Baron, R.; Ngan, C.H.; Ozonoff, D.; McCammon, J.A. and Vajda, S. Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem. Biol. Drug Design 2008 71 (2), 106-16. |
2008.04.11 | Jiang, Tao | Zhu, Green | Bayesian Networks | Peter J. Woolf, Wendy Prudhomme, Laurence Daheron, George Q. Daley and Douglas A. Lauffenburger.Bayesian analysis of signaling networks governingembryonic stem cell fate decisions. Bioinformatics 2006 21 (6), 741-753 |
2008.04.18 | McGillick, Brian | Rizzo Group | Lipid Membranes | Rosso, L. and Gould, I.R. Structure and dynamics of phospholipid bilayers using recently developed General All-Atom Force Fields. J. Comput. Chem 2008, 29, 24-37. |
2008.04.25 | Mukherjee, Sudipto | Rizzo Group | Parallel Computing, Drug Design | Amanda Peters, Marcus E. Lundberg, P. Therese Lang and Carlos P. Sosa. High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System. IBM Redpaper 2008 ibm.com/redbooks |
2008.05.02 | Palmer, Lance | Benach Group | Target Prediction | Qingliang Li and Luhua Lai, Prediction of potential drug targets based on simple sequence properties. BMC Bioinformatics 2007, 8, 353. |
2008.05.09 | Cornell, Wendy | Director: Molecular Systems, Merck Research Laboratories | Informal Round Table Discussion | What do group leaders look for in an applicant for a computational position in industry? |
2008.05.16 | Patsalo, Vadim | Green Group | Protein Design | Xiaozhen Hu, Huanchen Wang, Hengming Ke, and Brian Kuhlman, High-resolution design of a protein loop. PNAS2007, 104, 17668-17673. |