New Protein Sequence Analysis Server

James V. White jvwhite at tasc.com
Fri Mar 17 11:31:58 EST 1995


ANNOUNCING A NEW EMAIL SERVER FOR ANALYZING AMINO ACID SEQUENCES

The Protein Sequence Analysis (PSA) system, now accessible via
email at psa-request at darwin.bu.edu, estimates the tertiary
structural class and secondary structure of a protein from its
amino acid sequence. The PSA system is intended for
nonhomologous sequences that are unlike any other sequences in
the sequence databanks. The PSA system is currently based on 15
families containing 209 probabilistic Discrete State-space
Models (DSMs), which are intended to represent the major folding
classes in J.  Richardson's taxonomy of tertiary structural
domains.

The PSA server is maintained at the BioMolecular Engineering
Research Center of Boston University. For information on usage,
send an empty email message to psa-request at darwin.bu.edu with
the word "help" in the subject field.

The analysis algorithm is based on optimal filtering and
smoothing algorithms as described in the paper "Structural
analysis based on state-space modeling" by C.M. Stultz, J.V.
White, and T.F. Smith, Protein Science (1993), 2, 305-314. The
mathematical basis for the models and algorithms is presented in
"Protein Classification by Stochastic Modeling and Optimal
Filtering of Amino-Acid Sequences," by J.V.  White, C.M.
Stultz, and T.F. Smith, Mathematical Biosciences (1994), 119,
35-75.



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