THREADER 2 - Fold Recognition Software

David Jones jones at
Tue Jan 28 11:30:18 EST 1997


Protein Bioinformatics Group
University of Warwick

A new version of THREADER has just been released.

THREADER / THREADER 2 are programs for predicting protein tertiary
structure by recognizing the correct fold from a library of alternatives.
Of course if a fold similar to the native fold of the protein being
predicted is not in the library, then this approach cannot succeed.
Fortunately, however, certain folds crop up time and time again, and so
fold recognition methods for predicting protein structure can be very
effective (as demonstrated at CASP1 and CASP2).

The main new features of THREADER 2 are as follows:

* New statistical tests for enhancing the reliability of predictions.

* Allows secondary structure information to be included in the threading
  process. So, if you have a reasonable idea of the secondary structure
  of your protein, you can now use that information to good effect.

* Very extensive domain based fold library plus domain recognition options.

* Sequence weighting for modelling remotely related proteins.

* Alternative sequence-structure alignment algorithms built in.

Some other new features are included but not yet documented until
they are tested properly.

THREADER 2 can be obtained via the following WWW URL:

This message was written, produced and executively directed by Dr David Jones
Address: Dept. of Biological       |   Email: jones at
Sciences, University of Warwick,   |     Tel: +44 1203 523729
Coventry CV4 7AL, U.K.             |     Fax: +44 1203 523568

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