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Table 10.7. Threading servers and program sources
Program   Web address   Method   Reference
123D contact potentials between amino acid side groups Alexandrov et al. (1996)
3D-PSSM new sequence–structure using position-specific scoring matrices Russell et al. (1997)
GenTHREADER expands a threading approach using neural networks by adding sequence similarity in different genomes Jones (1999); McGuffin and Jones (2003)
Honig lab threading methods using biophysical properties see Web site
Libra I
new target sequence and 3D profile are aligned by dynamic programming Ota and Nishikawa (1997)
NCBI structure site Gibbs sampling algorithm used to align sequence and structurea Bryant (1996)
Profit fold recognition by the contact potential method M. Sippl (see Web site)
PSIPRED Home of several protein analysis tools including threaders McGuffin and Jones (2003)
Threader 3.4 prediction by recognition of the correct fold from a library of alternatives Jones et al. (1995)
TOPITS 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 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
    a Program has to be set up on a UNIX server.


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