Server Help File
Prediction of Protein Secondary Structure
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For a limited time, test version of the new algorithm for the prediction
of protein secondary structure will be available through the E-mail server.
Algorithm does not use multiple alignments or other homology/evolutionary
related information and does not implement neural network techniques. It
was designed primarily to handle predictions for the proteins which do not
have any significant homology with proteins currently available in PDB.
To access the server, send e-mail message containing amino acid sequence
of your protein to the address
bio at margit.scri.fsu.edu
Message should contain:
1. Context -SSP- (Secondary Structure Prediction) in the Subject Line;
2. String -#START- immediately preceeding strings with amino acid sequence;
3. Strings with amino acid sequence;
4. String -#END- immediately following strings with amino acid sequence;
5. No non-aminoacid symbols (except of possible formatting blanks and digits)
in the strings between #START and #END strings.
Example of message body:
---------------------------- example start ------------------------------
#START
PKPIFREYIGVKPNSTTLHD FPTEIINTET LEFHYILGFA IESYYESGKG TGTFEESWDV
ELFGPEKVKN L K R R H P EVKV VISIGGRGVN TPF
#END
----------------------------- example end -------------------------------
Server is VERY experimental, but I hope that all incoveniences might
be compensated by the high prediction accuracy. Installed on the server
model of the secondary structure organization will be updated in the process
of ongoing model refinement. Prediction accuracy probably will increase,
therefore update your results using latest model version. Due to the low
restart frequency of the server, delays up to 20 minutes in the return of
results should be expected.
Note that algorithm have a limited accuracy in analysis of short (less
than 60aa) and artificial sequences (like polypeptides with highly biased
amino acid composition and/or with artificial pseudo-regularities).
For helpful comments, send messages to strelets at scri.fsu.edu.
Dr. Victor B.Strelets
Supercomputer Computations Research Institute
400 Science Center Library
FSU B-186, Tallahassee, FL 32306
Ph. (904) 644-6563
FAX (904) 644-0098 (Attn: Dr. Strelets)
