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


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


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.