2006-2007 AMS-532 Fall-Spring

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.