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Running D. Eisenberg's 3D-profile programs and the GCG package

The source files are in /srv/local/eisenberg
The executable files are in /srv/local/eisenberg 

It needs a .pdb file and a file with secondary structure endpoints;
Secondary structure file is NOT free format - do it exactly as 
  in the PDB, except that the only things read are "SHEET" 
  or "HELIX", and res #'s.

environments  - input your coordinators & amp; secondary 
		  structure - assigns environments

verify_3d  - reads the output of environments
                - scores your sequence vs. your structure, averaged 
		       over a variable length window
                - output = a ".plotdat" file, renumbered, unfortunately.
                  renum_plotdat. for is my little dittie to restore meaningful
                       sequence #'s before plotting with curvy - see the
                       commentary at the top of the code.

profiler_3d     - reads the output of environments
                - writes a profile file ".prf" that can be read by search.com
                       OR by the GCG Wisconsin sequence database package.
		- The search.com is a command program in csbgln, a VAX/VMS system. 
		  Currently we don't have the GCG available in this Unix system, please
		  ask Pat Fleming for more infomation about GCG.

References for 3d profiles:

        Bowie, J.U., Luethy, R., and Eisenberg, D.
        "A Method to Identify Protein Sequences that Fold into a Known
        Three-Dimensional Structure"
        Science 253, 164-170 (1991).

        Luethy,R., Bowie,J.U., and Eisenberg,D. (1992)
        "Assessment of protein models with three-dimensional profiles",
        Nature 356, 83-85 (1992)

References for profiles in general:

        Gribskov, Michael, McLachlan, Andrew D., and Eisenberg, David,
        "Profile analysis: Detection of distantly related proteins",
        Proc. Natl. Acad. Sci. (USA) 84, 4355-4358 (1987).

        Gribskov, M., Luethy, R., and Eisenberg, D., "Profile
        Analysis", in Methods in Enzymology, R.F. Doolittle,
        ed.,  Academic press, Vol. 183, 146-159 (1990).

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Last Modified: Friday, 26-Mar-1999 16:15:44 EST by P. Fleming