Protein loops

Don & bashford at
Tue Jul 20 20:08:03 EST 1993

I don't know of computer programs specifically designed to do what you
want, but many of the scientific issues you touch on, how to fit in
a new loop, what to do about sidechain clashes, etc, have been studied
in great detial by Neena Summers, now at Monsanto in St. Louis
(safe and dry, I hope).  

As a starting point, I suggest:
Summers & Karplus (1990) J. Mol. Biol. 216:991
Summers & Karplus (1989) J. Mol. Biol. 210:785

Summers used a series of CHARMM scripts rather than any systematic
program for her purposes.

Some earlier work along these lines was done by Alwyn Jones, the creator
of the FRODO graphics package.  Perhaps he has a program available.
[Jones & Thirrup (1986) EMBO J. 5:819.]

Donald Bashford
Dept. Mol. Biol.
Scripps. Res. Inst.
bashford at

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