BetaWrap / BetaWrapPro
BetaWrap is a program that scores sequences for compatibility with the right-handed beta-helix fold. It incorporates structural features of the known beta-helix structures, as well as residue pair preferences learned from beta-sheets in non-beta-helices, to generate and score potential wraps of a query sequence into a beta-helical structure. It computes a score and P-value which reflect how well a query sequence fits into the structural template, and returns the top-scoring parses of the sequence into multiple rungs.
The BetaWrapPro program predicts right-handed beta-helices and beta-trefoils by using both sequence profiles and pairwise beta-strand interactions, and returns coordinates for the structure.
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BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.
Bradley P, Cowen L, Menke M, King J, Berger B.
Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14819-24.
Proteins. 2006 Jun 1;63(4):976-85.
Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins.
McDonnell AV, Menke M, Palmer N, King J, Cowen L, Berger B.