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From: dd@beta.UUCP (Dan Davison)
Newsgroups: sci.bio
Subject: Protein "shape" prediction
Message-ID: <10537@beta.UUCP>
Date: Fri, 25-Sep-87 16:25:11 EDT
Article-I.D.: beta.10537
Posted: Fri Sep 25 16:25:11 1987
Date-Received: Sun, 27-Sep-87 01:47:00 EDT
Organization: Los Alamos Natl Lab, Los Alamos, N.M.
Lines: 37
Keywords: lotsa work, little known


.Does anyone out there know of a good textbook summarizing laboratory
.techniques used in molecular biology?  

Try "Molecular Cloning" by Tom Maniatis et al, Cold Spring Harbor Press,
about 1984.  There are some hysterical errors in it, but it's an excellent
overview and in general the most commonly cited for these techniques.  IRL
Press (Oxford and Washington DC) has a "Practical Techniques in blah"
series (gel electrophoresis, sequencing, and cloning are the three that I
can immediately recall).  I haven't used the latter so I can't comment on
the quality.  Anyone else out there (Craig? Dizzy Dan? Sean?) remember the
name of the new competitor to "Molecular cloning"?  It has come out recently
and I've heard good things about it, but a quick scan of the latest PNAS
does not reveal any references to it.  

.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)?

If you mean tertiary structure by "shape", yes some; if you mean secondary
structure (alpha helices, beta sheets, beta turns) lots and lots.  For the
former, see the paper by Richard A. Lathrop, Teresa Webster, and Temple

Smith (or some permutation of those authors) in PNAS, or MIT AI Labs Memo
902, "Ariadne: pattern directed inference and hierarchial abstraction in
protein structure recognition" (May 1987).  The Webster, Lathrop, and Smith
paper may be in Biochemistry, but may not be out yet.  The AI memo dated May
says "To appear".  The AI memo is copyrighted ACM so it may be published
somewhere, but I don't follow non-biological literature.

There are also lots of people doing molecular mechanics attempts at tertiary
structure, but the number of variables is so large that according to one
estimate you'd need thousands of Cray-2s running in parallel and many, many,
many total universe lifetimes to calculate just one small protein (100 amino
acids).

dan davison/theoretical biology/t-10 ms k-710/los alamos national laboratory
los alamos, nm 87545/ dd@lanl.gov (arpa)/...cmcl2!lanl!dd (uucp)