Protein threading is one of the powerful methods for protein structure prediction. Some advances are recently made by the significant utilization of distance restraints. Xu et al. proposed a protein threading method in which distance constraints obtained from NMR experiments were taken into account [5]. Young et al. recently developed a novel experimental method to increase the predictive accuracy of the fold recognition method by using chemical cross-linking and time-of-flight (TOF) mass spectrometry to identify LYS-LYS cross-links [6]. Though Xu et al. considered protein threading with pairwise contact energy and constraints [5], threading with profiles is also known as a powerful method for protein structure prediction. In particular, PSI-BLAST is widely used both for sequence similarity search and protein structure prediction [3]. Therefore, we have recently developed two algorithms for computing optimal threadings with profiles and constraints [1]. In this short abstract, we show performances of these two algorithms.
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