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From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.molbio.proteins
Subject: Re: protein design using computational methods
Keywords: protein folding, computational methods, molecular dynamics
Message-ID: <2158@fcs280s.ncifcrf.gov>
Date: 14 May 91 14:13:09 GMT
References: <719@mixcom.COM>
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In article <719@mixcom.COM> mmvvmm@mixcom.COM (Daniel Offutt) writes:

> ... I have yet to discover an article concerning the application of
> computational methods to protein *design*.

@article{Blundell1985,
author = "T. Blundell
 and M. J. E. Sternberg",
title = "Computer-aided design in protein engineering",
journal = "Trends in Biotechnology",
volume = "3",
pages = "228-235",
year = "1985"}

@article{Wetzel1986,
author = "R. Wetzel",
title = "What is protein engineering?",
journal = "Protein Engineering",
volume = "1",
pages = "3-5",
year = "1986"}

@article{Pabo1983,
author = "C. Pabo",
title = "Molecular Technology: Designing proteins and peptides",
journal = "Nature",
volume = "301",
pages = "200",
year = "1983"}

There must be more recent papers than these, perhaps you can
use them as the basis of a search.

> Perhaps this should not be surprising, since a solution to the
> folding problem appears to be a prerequisite to a solution to the general
> protein design problem, and the folding problem appears to be computationally
> intractable today.  Is this an accurate summary of the state of the art in
> computational protein design?

No, there have been several attempts reported in the literature, even a case of
a the construction of a catalytic protein.  Sorry, I don't have that reference,
but I think there was a paper in nature within the last year.  Dickerson, I
believe, has been working on constructing bundles of alpha helices and beta
sheets.  Also, the the emerging field of nanotechnology, it is recognized that
it well may be easier to design proteins from scratch than to figure out how
they evolved in nature.  Look at the sci.nanotech news group for discussions.

@article{Drexler1981,
author = "K. E. Drexler",
title = "Molecular engineering: An approach to the development
of general capabilities for molecular manipulation",
journal = "Proc. Natl. Acad. Sci. USA",
volume = "78",
pages = "5275-5278",
year = "1981"}

@book{Drexler1986,
author = "K. E. Drexler",
title = "Engines of Creation",
publisher = "Anchor Press",
address = "Garden City, New York",
year = "1986"}

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov