Protein Structure Prediction Using Web E-Mail Server

Bill Schmidt schmidt at
Mon Jun 5 12:47:59 EST 1995


The previously announced Protein Sequence Analysis (PSA) e-mail server
now has a Web interface.  The URL is 

The PSA server analyzes your protein sequence and determines which 
of 209 sequence-structure models, spanning 15 different protein folding
classes, are the most probable explanations of your sequence.  The
analysis results (PostScript files depicting the folding-class
probabilities and secondary-structure probabilities) are returned to
you by e-mail.

The PSA e-mail server is particularly suited for analyzing novel
sequences that are unlike any others in the sequence databanks.
Currently, the PSA is based on a set of probabilistic Discrete
State-space Models (DSMs) that are intended to represent the major
folding classes in J.  Richardson's taxonomy of tertiary structural

The PSA e-mail server is maintained at the BioMolecular Engineering
Research Center of Boston University. If you don't have a forms-capable
Web browser (e.g., Netscape), you may obtain usage information by 
sending an empty email message to psa-request at with the 
word "help" in the subject field.

The PSA 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.

Bill Schmidt
Interface Specialist
BioMolecular Engineering Research Center
schmidt at

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