View source for 2006-2007 AMS-532 Fall-Spring

== Journal Club Participants, Topics, References, and Schedule ==
Note: Each participant please update the Wiki as required

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| '''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.
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| 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.
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| 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.
|-

|- style="background:lightgreen"
| '''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.
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