From: richard@frej.scs.uiuc.edu (Richard A. Goldstein)
Newsgroups: bionet.biology.computational
Subject: Re: neural nets and protein structure prediction
Date: 15 Apr 92 05:09:26 GMT
Article-I.D.: ux1.1992Apr15.050926.10263
Distribution: bionet
Organization: School of Chemical Sciences Univ. of Illinois, Urbana IL
Originator: biocomp@lerkim.umiacs.umd.edu

In article <1992Apr14.184510.9403@dartvax.dartmouth.edu> robert.h.gross@dartmouth.edu (Robert H. Gross) writes:
>Hi folks,
>
>I am interested in identifying some recent papers that address the use
>of neural nets in determining protein structure. Can someone please
>post some references?
>
>Thanks.
>
>Bob Gross
>Dartmouth College
>bob.gross@dartmouth.edu

We have been at work developing ways to use Hopfield Neural Networks to
predict protein tertiary structure.  See:

        Author = Mark S. Friedrichs and Peter G. Wolynes,
        Title = Toward Protein Tertiary Structure Recognition by
                 Means of Associative Memory Hamiltonians,
        Journal = Science,
        Year = 1989,
        Volume = 246,  
        Pages = 371-373

        Author = Mark S. Friedrichs and Peter G. Wolynes,
        Title = Molecular Dynamics of Associative Memory Hamiltonians
                 for Protein Tertiary Structure Recognition,
        Journal = Tetra. Comp. Meth.,
        Year = 1991,
        Volume = 3,
        Pages = 175-190 

        Author = Mark S. Friedrichs and Richard A. Goldstein
                and Peter G. Wolynes,
        Title = Molecular Dynamics of Associative Memory Hamiltonians
                 for Protein Tertiary Structure Recognition,
        Journal = J. Mol. Biol.,
        Year = 1991,
        Volume = 222,
        Pages = 1013-1034 

        Author = Richard A. Goldstein and Zan Luthey-Schulten and
                and Peter G. Wolynes,
        Title = Optimal Protein Folding Codes from Spin-Glass Theory,
        Journal = PNAS,
        Year = 1992,
        Note = in press (Next month, I think)

Also see the references contained in these papers, especially the JMB paper.
Other work using feed-forward neural networks for tertiary structure
prediction has been done by:

        Author = H. Bohr and J. Bohr and S. Brunak and R. M. J. Cotterill
                  and B. Lautrup and L. Norskov and O Olsen
                  and S. Petersen,
        Year = 1990,
        Title = A Novel Approach to Prediction of the 3-dimensional
                 structure of Protein Backbones by Neural Networks,
        Journal = FEBS Lett.,
        Volume = 261,
        Pages = 43-46

        Author = G. L. Wilcox and M. Poliac and A. Brugge and
        M. N.  Liebman,
        Journal = Tetra. Comp. Meth.,
        Title = Neural Network Analysis of Protein Tertiary Structure,
        Volume = 3,
        Pages = 191-211

Probably more work has been done on secondary-structure prediction:

        Author = N. Qian and T. J. Sejnowski,
        Year = 1988,
        Journal = J. Mol. Biol.,
        Title = Predicting the secondary sequence of globular proteins
                 using neural network models,
        Volume = 202,
        Pages = 865-884

        Author = L. H. Holley and M. Karplus,
        Year = 1989,
        Title = Protein Secondary Structure Prediction with a
                 Neural Network,
        Journal = PNAS,
        Volume = 86,
        Pages = 152-156

        Author = H. Bohr and J. Bohr and S. Brunak and R. M. J. Cotterill
                  and B. Lautrup and L. Norskov and O Olsen
                  and S. Petersen,
        Year = 1988,
        Title = Protein Secondary Structure and Homology by Neural
                 Network--The $\alpha$-helices in Rhodopsin,
        Journal = FEBS Lett.,
        Volume = 241,
        Pages = 223-228 

        Author = D. G. Kneller and F. E. Cohen and R. Langridge,
        Title = Improvements in Protein Secondary Structure Prediction
                By an Enhanced Neural Network,
        Journal = J. Mol. Biol.,
        Volume = 214,
        Year = 1991,
        Pages = 171-182

Hope this helps.

                                         Richard Goldstein
                                         richard@frej.scs.uiuc.edu