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Thursday, July 28, 2005

pattern for 1.1.1 another approch

hard to find pattern using POSA or SSM
so I use our methods,
get interlock strands by using getinterlockstr.pl
retrieve sequences by using getinterlocksq.pl
alignment S1 using genedoc, adj out liner manually by conserved sequences/properties.
then I get this pattern

[FILMVY]-[KLPRSTVYG]-[CV]-X(2,30)-{CEIMPVW}-[VW]-{AGHRDNST}-X(20,60)-[FILMVT]-{CFINPSWY}-[FHILM]-X(2,30)-{CFKPQW}-Y-{ACDGKMPRV}-[CLMRVD]

try these on scanprosite

1bww-a
1cd0-a
1h5b-a
1akj-d
1vge-h
1kxq-e
1neu
1pko-a
1hnf
1dr9-a
1ncn-a
1eaj-a
1cdy
1ccz-a
1qfo-a
1nko-a
1f97-a
1hkf-a
1l6z-a
1i8l-c
1jma-a

next time, I'll try hydrogen bond alignment.

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