In article <1992Apr14.184510.9403 at dartvax.dartmouth.edu> robert.h.gross at 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 at 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 at frej.scs.uiuc.edu
