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Ron Cole rcole at LEUCINE.NCSA.UIUC.EDU
Mon Sep 6 21:06:29 EST 1993


Subject: alignment of predicted secondary structure

Hello,
        This is a summary concerning the alignment of predicted secondary 
structure.  I would like to thank all who wrote me with advice and information,
and apologize for taking so long to write up this summary.

        I did not find any programs which directly combined the output of 
PILEUP and PEPTIDESTRUCTURE, however I did obtain the following items;

1.)     Dr. Alfred Beck of the Max-Plank-Institut, sent me his program, 
        PREDICT MULTI.  This installed easily into GCG version 7.0, and does
        the following;
        "Predict__Multi makes secondary structure predictions for aligned
        peptide sequences according to the Chou-Fasman method. All secondary
        structure predictions and an average are displayed above each other."

        I think there is significant interest, and I hope that Dr. Beck's
        program is incorporated into the standard GCG package.
        Dr. Beck can be reached at Beck at MPIMG-BERLIN-DAHLEM.MPG.DE      
        
2.)     I sent a one word message, HELP, to PredictProtein at EMBL-Heidelberg.DE
        This mail server will accept a protein sequence, and then perform a 
        multiple alignment and secondary structure prediction.  Dr. Schneider
        has informed me that soon this mail server should have the ability to 
        receive MSF (multiple sequence format) files soon.  For more info,
        one should mail the PredictProtein server as I did, and read the article
        "Database of Homology-Derived Structures and the Structural Meaning of 
        Sequence Alignment", by Sander, Chris &  Schneider, Reinhard,
        Proteins, Vol. 9, pp. 56-68, 1991

3.)     Dr. Doelz informed me that;
 
     "PLOTALIGN takes a GCG format sequence alignment,  and plots  the mean
     and  range of  values for any amino acid parameter you  supply.   The
     "panel  file" contains a list of  parameters to be plotted.  The main
     database of  parameters is  taken from Nakai et al.  (1988),  and the
     default panel file uses selected  parameters  from  the  13  discrete
     clusters   in   that  paper.   This  program  is  experimental.   Any
     suggestions would be most welcome."

        However, "plotalign is on the UNIX CD distribution of GCG 7.1",
        so I do not have this available to me.


        I am quite new in this field, so I welcome any further comments.  I
thought that combining secondary structure prediction and alignment data might
be a way to get more information, and then I found out that people had been
doing it for quite some time.  An excellent article concerning this is 
"Predicting de novo the folded structure of proteins" by Dr. Benner (Curr. 
Opinion in Structural Biology, vol 2, 402-418, 1992).  In this article 
Dr. Benner writes this concerning this approach;

        "When applying such a strategy, one hopes that the errors made by the
predictive method behave as noise, and are averaged out by multiple samplings.
This assumption appears to be satisfied for alpha/beta-barrel proteins in
general but not for other families of proteins." 

Thank you very much,  
Skip Cole

*************************************************************************
* Skip Cole             *       The three graces of a scientist are     *
* rcole at ncsa.uiuc.edu   *       objectivity, clarity and compassion.    *
* (217)355-5308         *       The greatest of these being compassion. *
*************************************************************************




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