ProblemA3-3 - Computational Biology 03-310, Spring 2006 R....

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Unformatted text preview: Computational Biology 03-310, Spring 2006 R. F. Murphy Page 1 of 1 Problem A3 Predicting and viewing protein structure Due: February 28, 2006 For this assignment you are given the amino acid sequence of a chimeric protein (a chimera in this context is defined as a macromolecule composed of pieces from other macromolecules). The sequence is in a FASTA format file chimera06.fa on the Homework Problems web page. Hand in requested printouts and written answers (with justifications) to the questions. Label your answers clearly. Questions (Total of 40 points) 1. Use the server at http://fasta.bioch.virginia.edu/fasta_www/chofas.htm to predict secondary structure for the chimera using the Chou-Fasman method. (Save the results for use in part 4 below.) What amino acids are part of the longest region that is predicted to be alpha helix? 2. Use the BLAST server to determine what proteins were used in creating the chimera, and find 3D structures for each. Make a table containing five columns: (1) the names of the individual proteins whose fragments for each....
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