simulation of protein folding process (paper)

raffaele at caio.irmkant.rm.cnr.it raffaele at caio.irmkant.rm.cnr.it
Tue May 2 12:07:59 EST 1995


sent on 2/5/95 at 5 p.m to:
connectionists
gann
biosci: computational biology
        molecular modelling 
------------------------------


FTP-host:       kant.irmkant.rm.cnr.it 
FTP-filename:  /pub/econets/calabretta.folding.ps.Z


The following paper has been placed in the anonymous-ftp archive
(see above for ftp-host) and is now available as a compressed
postscript file named

          calabretta.folding.ps.Z     (14 pages of output)

The paper is also available by World Wide Web:
http://kant.irmkant.rm.cnr.it/gral.html

It will appear in Proceedings of 3rd European Conference on
Artificial Life (Granada, Spain, 4-6 June 1995).
Comments welcome.

     Raffaele Calabretta

email address:                  raffaele at caio.irmkant.rm.cnr.it

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    "An Artificial Model for Predicting the Tertiary Structure
     of Unknown Proteins that Emulates the Folding Process"

    Raffaele Calabretta, Stefano Nolfi, Domenico Parisi
    Department of Neural Systems and Artificial Life
    Institute of Psychology
    National Research Council
    V.le Marx, 15
    00137 ROME
    ITALY


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                      Abstract:

We  present  an  "ab initio"  method  that tries  to  determine the tertiary 
structure of unknown proteins by modelling the folding process without using 
potentials extracted from  known  protein  structures. We  have been able to 
obtain  appropriate  matrices  of  folding potentials, i.e. 'forces' able to 
drive the folding process  to  produce correct  tertiary structures, using a 
genetic  algorithm. Some  initial  simulations  that  try  to  simulate  the 
folding  process  of  a  fragment  of  the crambin that results in an alpha-
helix, have  yielded good results. We  discuss  some general implications of 
an  Artificial Life approach  to  protein  folding which makes an attempt at 
simulating the  actual  folding  process rather  than just trying to predict 
its final result.

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