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From: roy@phri.UUCP (Roy Smith)
Newsgroups: sci.bio
Subject: Re: Molecular Bio texts, protein shapes and computers
Message-ID: <2910@phri.UUCP>
Date: Fri, 25-Sep-87 22:23:51 EDT
Article-I.D.: phri.2910
Posted: Fri Sep 25 22:23:51 1987
Date-Received: Sun, 27-Sep-87 07:26:58 EDT
References: <2040@super.upenn.edu>
Reply-To: roy@phri.UUCP (Roy Smith)
Organization: Public Health Research Inst. (NY, NY)
Lines: 31

In article <2040@super.upenn.edu> li@linc.cis.upenn.edu (Siufai Li) writes:
> Does anyone know if someone is doing research involving the prediction of
> the shape of a protein from its amino acid sequence (or nucleotide sequence)?
> [...] I wonder if such a task is possible using computers.

	This is without a doubt one of the big open issues of computational
biology (does this field have an official name?)  Lots of people are
working on it, but as far as I know, nobody has had much success.  The
old standby is an algorithm described in:

%A P.Y. Chou
%A G.D. Fasman
%T Prediction of the secondary structure of proteins from their amino
acid sequence
%J Adv. Enzymol.
%V 47
%P 45-148
%D 1978

	Chou-Fasman is almost a decade old and pretty much worthless as an
analytical tool.  Yet, because not much better has come along, people still
use it (and, in my opinion, put far too much faith it the results).

	The ultimate goal is to take an amino acid sequence and predict not
only the 3-dimensional structure, but also the function of the resultant
enzyme, and its Km.  Not that I think this ever will happen, but it's nice
to dream.
-- 
Roy Smith, {allegra,cmcl2,philabs}!phri!roy
System Administrator, Public Health Research Institute
455 First Avenue, New York, NY 10016