TitleInteractive Protein Manipulation (In Proceedings)
inProceedings of the 2002 UC Davis Student Workshop on Computing, TR CSE-2002-28
Author(s) Oliver Kreylos, Bernd Hamann, Nelson Max, Wes Bethel, Silvia Noemi Crivelli
Year 2002
PublisherUniversity of California, Davis
AddressDavis, California
Abstract One of the grand challenges in computational biology is the prediction of the three-dimensional structure of a protein, which determines its function, from its chemical makeup alone. A protein’s primary structure, i. e., its amino acid sequence, is directly encoded in its DNA sequence,which is a purely one-dimensional structure that does not directly encode a three-dimensional shape. It is commonly believed that the “native” shape of a protein is the one corresponding to the global minimum of its internal energy; thus, the protein folding problem has been treated as an optimization problem in recent years. It is important to start solving any optimization problem from a “good” set of initial configurations that allow the optimization code to, ideally, search the complete optimization space for a global minimum. Our work focuses on providing an interactive, visual tool to rapidly create many initial configurations for a given amino acid sequence, which are then used as input for an optimization algorithm.