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Table 10.7. Threading servers and program sources
Program		Web address		Method		Reference
123D	http://123d.ncifcrf.gov	contact potentials between amino acid side groups	Alexandrov et al. (1996)
3D-PSSM	http://www.sbg.ic.ac.uk/~3dpssm/	new sequence–structure using position-specific scoring matrices	Russell et al. (1997)
GenTHREADER	http://bioinf.cs.ucl.ac.uk/psipred/	expands a threading approach using neural networks by adding sequence similarity in different genomes	Jones (1999); McGuffin and Jones (2003)
Honig lab	http://honiglab.cpmc.columbia.edu/	threading methods using biophysical properties	see Web site
Libra I	http://www.ddbj.nig.ac.jp/ search/libra_i-e.html	new target sequence and 3D profile are aligned by dynamic programming	Ota and Nishikawa (1997)
NCBI structure site	http://www.ncbi.nlm.nih.gov/	Gibbs sampling algorithm used to align sequence and structurea	Bryant (1996)
Profit	http://lore.came.sbg.ac.at/	fold recognition by the contact potential method	M. Sippl (see Web site)
PSIPRED	http://bioinf.cs.ucl.ac.uk/psipred/	Home of several protein analysis tools including threaders	McGuffin and Jones (2003)
Threader 3.4	http://bioinf.cs.ucl.ac.uk/threader/threader.html	prediction by recognition of the correct fold from a library of alternatives	Jones et al. (1995)
TOPITS	http://www.embl-heidelberg.de/predictprotein/	detects similar motifs of secondary structure and accessibility between a sequence of unknown structure and a known fold	Rost (1995a,b)
TOUCHSTONE		secondary and tertiary restraint prediction applied to ab initio folding	Kihara et al. (2001)
UCLA-DOE structure prediction server	http://fold.doe-mbi.ucla.edu	already above fold-recognition using a variety of sequence similarity and structure threading methods including DASEY (see text)	Fischer and Eisenberg (1996); Mallick et al. (2002)
Information on the research groups that work on structure prediction may be found at the CASP2 Web sites accessible at http://predictioncenter.llnl.gov/.     a Program has to be set up on a UNIX server.