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Wednesday, April 19, 2006

pattern for 3A from H-bond alignment

After add the missing K+3 strand
I got this pattern for 3A

[AHLMV]-X(6,9)-[AFILV]-x-[FILV]-x-[CL]-X(11,16)-[FGLW]-X(6,17)-[FILNV]-X(8,17)-[AEIKLST]-X(7,11)-[FILV]-x-[DILM]-X(9,11)-[ADEFHLNRT]-[FLY]-x-[CFLM]-X(13,16)-[HKLNQRVY]-[FLTV]-x-[ALRTV]-[FLQSTV]

when run on scanprosite, I got 169 hits, which is much better then last week.
although still have some false positive like: 1EIY-B, 1E6E-C, 1JJC-B, etc.
we should have some tools to test positive rates by given a PDBID list.

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