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Protein threading by PROSPECT: a prediction experiment in CASP3
Y Xu1, D Xu, O H Crawford
1Computational 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.
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 (