@article {bioinflmu-370,
	title = {{Improving fold recognition of protein threading by experimental distance constraints}},
	journal = {In Silico Biol},
	volume = {2},
	number = {3},
	year = {2002},
	pages = {325-337},
	abstract = {We present a comprehensive analysis of methods for improving the fold
recognition rate of the threading approach to protein structure prediction by the
utilization of few additional distance constraints. The distance constraints
between protein residues may be obtained by experiments such as mass spectrometry
or NMR spectroscopy. We applied a post-filtering step with new scoring functions
incorporating measures of constraint satisfaction to ranking lists of 123D
threading alignments. The detailed analysis of the results on a small
representative benchmark set show that the fold recognition rate can be improved
significantly by up to 30\% from about 54\%-65\% to 77\%-84\%, approaching the maximal
attainable performance of 90\% estimated by structural superposition alignments.
This gain in performance adds about 10\% to the recognition rate already achieved
in our previous study with cross-link constraints only. Additional recent results
on a larger benchmark set involving a confidence function for threading
predictions also indicate notable improvements by our combined approach, which
should be particularly valuable for rapid structure determination and validation
of protein models.},
	author = {Mario Albrecht and Daniel Hanisch and Ralf Zimmer and Thomas Lengauer}
}