Difference between revisions of "2006-2007 AMS-532 Fall-Spring"

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Latest revision as of 13:22, 15 September 2008

Journal Club Participants, Topics, References, and Schedule

Note: Each participant please update the Wiki as required

2006 Fall Participant Rotations or Research Group Topic References
2006.09.26 Mukherjee, Sudipto Rizzo Group scoring functions Wang, R.; Lu, Y.; Wang, S., Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 2003, 46 (12), 2287-303.
2006.10.03 Han, Ji Rizzo, Simmerling, Green MM-GBSA validation Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M., Validation and use of the MM-PBSA approach for drug discovery. J Med Chem 2005, 48 (12), 4040-8.
2006.10.10 Nieves-Gonzalez, Aniel Moore Group genetic networks Brandman, O.; Ferrell, J. E., Jr.; Li, R.; Meyer, T., Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 2005, 310 (5747), 496-8.
2006.10.17 Patsalo, Vadim Simmerling, Green, Rizzo replica exchange Hansmann,U. H. E., Parallel Tempering algorithim for conformational studies of biological molecules. Chem Phys Lett 1997, 281, 140-150.
2006.10.24 Balius, Trent Green, Rizzo, Simmerling protein design Gordon, B.; Mayo, S. L.,Radical Performance Enhancements for Combinatorial Optimization Algorithms Based on the Dead-End Elimination Theorem. J Comput Chem 1998, 19 (13) 1505-1514;

Dahiyat, B. I.; Sarisky, C. A.; Mayo, S. L., De novo protein design: towards fully automated sequence selection. J Mol Biol 1997, 273 (4), 789-96.

2006.10.31 Carrascal, Noel Rizzo Group protein-lig binding Tirado, J. and Jorgensen, W.L., Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein-Ligand Binding. J. Med. Chem. 2006,49 (20), 5880-4.
2006.11.21 Cheng, Jonathan Green Group protein design Baker001.pdf
2006.11.28 Mukherjee, Sudipto Rizzo Group scoring functions Zhang, C.; Liu, S.,Zhu, Q. and Zhou, Y.,A Knowledge-Based Energy Function for Protein-Ligand, Protein-Protein, and Protein-DNA Complexes. J. Med. Chem. 2005, 48 (7), 2325-35.
2006.12.05 Nieves-Gonzalez, Aniel Moore Group signal transduction Haugh, J.M., A Unified Model for Signal Transduction Reactions in Cellular Membranes. Biophys J. 2002, 82 (2), 591-604.
2006.12.12 Patsalo, Vadim Simmerling, Green, Rizzo RNA database Gan, H.H. et al., RAG: RNA-As-Graphs database—concepts, analysis, and features. Bioinformatics 2004, 20 (8), 1285-91.
2007 Spring Participant Rotations or Research Group Topic References
2007.02.16 Balius, Trent Green, Rizzo, Simmerling multi-scale simulations Liu, Y. et al.,A Multiscale Computational Approach to Dissect Early Events in the Erb Family Receptor Mediated Activation, Differential Signaling, and Relevance to Oncogenic Transformations. Ann. Biomed. Eng. 2007, 35 (6), 1012-25.
2007.02.23 Han, Ji Rizzo, Simmerling, Green protein design Ambroggio, X.I. and Kuhlman, B.,Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds, J. Am. Chem. Soc. 2006, 128 (4), 1154-1161.

Ambroggio, X.I. and Kuhlman, B., Design of protein conformational switches. Current Opinion in Struc. Bio. 2006, 16 (4), 525-30.

2007.03.16 Mukherjee, Sudipto Rizzo Group scoring functions Lee., M.R. and Sun, Y., Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring. J. Chem. Theory Comput. 2007, 3 (3), 1106-119.
2007.03.30 Patsalo, Vadim Simmerling, Green, Rizzo synthetic biology Wang, B.; Papamichail, D.; Mueller, S.; Skiena, S. Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences. Natural Computing 2007, 6 (4), 359-70.
2007.04.13 Shipman, Jerry Rizzo protein folding Rhee, Y.M.; Sorin, E.J.; Jayachandran; Lindahl, E.; Pande, V.S. Simulations of the role of water in the protein-folding mechanism. Biophysics 2004, 101 (17), 6456-61.
2007.04.20 Chachra, Ricky Rizzo charge optimization Armstrong, K.A.; Tidor, B. and Cheng, A.C. Optimal charges in lead progression: A structure-based neuraminidase study. J. Med. Chem. 2006, 49, 2470-77.
2007.04.27 Balius, Trent Green, Rizzo, Simmerling multi-scale simulations Bhalla, U.S. and Iyengar, R. Emergent properties of networks of biological signaling pathways. Science 1999, 283 (5400), 381-7.
2007.05.08 Carrascal, Noel Rizzo Group protein rational design Green, D.F.; Dennis, A.T.; Fam, P.S.; Tidor, B. and Jasanoff, A. Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry 2006, 45 (41), 12547-59.