Subject: Re: Protein folding,structure prediction

From: [email-masked] (Mark Dalton)
Date: Wed, 21 Sep 1994 11:58:59 -0700 (MDT)

For predicting 3D Structure of proteins from a primary sequence.
(I still have a list of places to get 3D searching, i.e. comparison
 of 3D structures, if anyone needs the list).

Thanks!

Mark

Here is the information I have:

	Steven Brenner - Has given a couple of presentations at
	various confernences on a package he has been working on.
	Steven is from Cambridge Univ.

For predicting 3D structures from primary sequences.
SeqSee - Science( 258:p1369)
	or ftp canopus.biochem.ualberta.ca
        A suite of programs for protein sequence analysis
 
ProfileScan- forming a profile for given aligned sequences.
        by Michael Gribskov [email-masked] (formerly of
        one of the National Labs in the US).
Scrutineer - a protein sequence motif analysis program
You also may want to look into Scrutineer you can get it at:
                        [email-masked]
 
Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile
analysis: detection of distantly related proteins. PNAS USA 84,
4355-4358.
 
Gribskov, M., Methods in Enzymology (1990) 183, PP 146-159

URL = http://pscinfo.psc.edu/general/software/cray/c90/profiless/profiless.html
PROFILE-SS is a program that combines the optimal local sequence alignment
algorithm developed by Michael Watterman and Mark Eggert and the Profile
analysis methods of Gribskov into one program that finds the N-best alignments
between a database sequence and a profile. 

Bohr, H. and Bohr, J. and Brunak, S. and Cotterill, R. M. J. and
        Fredhom, H. and  Lautrup, B. and Petersen, S. B.
	"A Novel Approach to Prediction of the 3-Dimensional Structures
	of Protein Backbones by Neural Networks", FEBS Letters.
	Vol. 261, 1990, pages 43-46

Fetrow, J. S.; Bryant, S. H. New programs for protein tertiary structure
    	prediction.  Bio/Technology   1993, 11, 479-484.

Greller, L. D. and Steeg, E. W. and Salemme, F. R., "Neural Networks
	for the Detection and Prediction of 3D Structural Do
	mains in Proteins", Proceeedings Eighth International Conference
	on Mathematical and Computer Modelling. April, 1991.
	(A new version was submitted to Science).

Goel, N., Rouyanian, B. and Sanati, M. 1982. On the computation of the
	tertiary structure of globular proteins. III. Interresidue
	distances andS computed structures. J. Theor. Biol. 99:705-757.

Jameson, B.A. and Wolf, H. 1988. The antigenic index: a novel algorithm
	for predicting antigenic  determinants.  CABIOS 4:181-186.
	Janin, J. 1979. Surface and inside volumes in globular proteins.
	Nature 277:491-492.

Wodak, S. J.; Rooman, M. J. Generation and testing protein folds.  Curr.
    	Opinion Struct. Biol.   1993, 3, 247-259.

- 
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