Computational Approaches for Prediction of Cross Reactivity in Human Protein Kinome
Sridhar Maddipati1, Ariel Fernandez2 and Sangtae Kim1, (1)School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN 47906, (2)Bioenegineering, Rice University, 6100 Main Street, Houston, TX 77005 |
Separating True Positive Residue Contacts from False Positive Ones in Proteins, Using Constrained Metropolis Monte Carlo Simulations
Spyridon Vicatos, Chemical Engineering and Materials Science, University of Minnesota, 407 7th Street SE #215, Minneapolis, MN 55414 and Yiannis N. Kaznessis, Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Ave SE, Minneapolis, MN 55454 |
Atomic Molecular Dynamics of Blood-Clotting Proteins
Coray M. Colina1, Robert E. Duke2, Lalith Perera3, Tom Darden3 and Lee Pedersen3, (1)Department of Materials Science and Engineering, Pennsylvania State University, 121 Steidle Building, University Park, PA 16802, (2)Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, Raleigh, NC 27709, (3)National Institute of Environmental Health Science, Research Triangle Park, Raleigh, NC 27709 |
W-Sift, a Structural Interactions Based Potency-Wise Screening Technique for Protein-Small Molecule Complexes
Ravi Nandigam1, Claudio Chuaqui2, Juswinder Singh2 and Sangtae Kim1, (1)School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN 47906, (2)Computational Drug Design group, Biogen Idec, 14 Cambridge Ctr, Cambridge, MA 02135 |
Microarray Data Mining: A Novel Optimization-Based Iterative Clustering Approach to Uncover Biologically Coherent Structures
Meng Piao Tan1, James R. Broach2 and Christodoulos A. Floudas1, (1)Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, (2)Department of Molecular Biology, Princeton University, Princeton, NJ 08544 |
Optimization Based Automated Curation of Metabolic Reconstructions
Vinay S. Kumar, Department of Industrial Engineering, The Pennsylvania State University, 147A, Fenske Lab, University Park, PA 16802, Madhukar S. Dasika, Department of Chemical Engineering, Penn State University, 147A Fenske Lab, University Park, PA 16802, Priti Pharkya, The Pennsylvania State University, 147 Fenske Laboratory, University Park, PA 16802, Anthony Burgard, Genomatica, Inc., 5405 Morehouse Drive Suite 210, San Diego, CA 92121 and Costas D. Maranas, Department of Chemical Engineering, The Pennsylvania State University, 112, Fenske Lab, University Park, PA 16802 |
In Silico Modification of a Bistable Genetic Network to Obtain Oscillatory Expression Patterns
Sergio Iadevaia, Chemical and Biomolecular Engineering, Rice University, Houston, TX 77005 and Nikos Mantzaris, Chemical & Biomolecular Engineering, Rice University, 6100 Main Street MS#362, Houston, TX 77005 |
Evolution and Changes in the Blosum Matrix and Blocks Database
Mark Styczynski, Chemical Engineering, MIT, 66-264 MIT 77 Massachusetts Ave, Cambridge, MA 02139, Kyle L. Jensen, MIT, 66-264 MIT 77 Massachusetts Ave, Cambridge, MA 02139 and Gregory N. Stephanopoulos, Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., 56-439, Cambridge, MA 02139 |
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