Protein threading by PROSPECT: a prediction experiment in CASP3 |
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| Authors: | Xu Y Xu D Crawford O H Einstein Larimer F Uberbacher E Unseren M A Zhang G |
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| Institution: | Computational Protein Structure Group, Computational Biosciences Section, Life Sciences Division and Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830. |
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| Abstract: | We present an analysis of the protein fold recognition experiment using PROSPECT in The Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP3). PROSPECT is a computer program we have recently developed for finding an optimal alignment between a protein sequence and a protein structural fold. Two unique features of PROSPECT are (a) that it guarantees to find the globally optimal sequence-structure alignment and does so in an efficient manner, when the alignment-scoring function consists of three additive terms: (i) a singleton fitness term, (ii) a pairwise contact preference term between residues that are spatially close (
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