2007-2008 AMS-532 Fall-Spring

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.