I have just updated the page for the first time in a few years.
There are a few new and updated links, and all the dead links have (I hope)
been pruned. I'm thinking that I might move this page on to our main server
soon - but I will put a redirect here if I do. As always, comments and suggestions
are most welcome.
Version 2.0b1 is available to download now. MacStripe
is the ideal tool for anyone who wants to explore potential alpha-helical
coiled coils in the sequence of their protein. With a full Macintosh interface,
the results of analyses (raw data or publication quality plots) can easily
be exported to other software. The "Inspector" window acts like a magnifying
glass so you can study your protein on a residue-by-residue basis. MacStripe
uses the algorithm of Andrei Lupas's COILS2 for detailed
and reliable coiled-coil predictions.
This home page is intended as a resource for people who want to analyse protein
sequences and structures for the presence of alpha helical coiled-coils. The aim
is to make conveniently available all the known software and Web resources in
a single location. No doubt there will be many omissions- please let
me know if there is anything else you would like to see included.
This was the first useful algorithm for predicting coiled coils in protein sequences.
The reference is: Lupas, A., M. Van Dyke, and J. Stock, "Predicting Coiled Coils
from Protein Sequences." Science,
1991. 252: p. 1162-1164.
MacStripe:
my own coiled-coil prediction program for the Macintosh. The current version
is 2.0b1. The ideal tool for interactive exploration of your protein's coiled-coils
(if you are lucky enough to own a Macintosh computer).
Andrei Lupas himself has improved upon his original algorithm (Lupas, A.
(1996) Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology
266: 513-525). His software is available by ftp.
Versions are available for DOS, UNIX and VMS together with source code.
There is also a COILS web
server at EMBnet in
Switzerland. This allows you to paste in your sequence and get both graphical
and numeric results.
Andrei Lupas's COILS documentation (converted
to HTML). This is useful not only for COILS users but also for MacStripe users,
particularly with respect to the interpretation of the results.
Paircoil and Multicoil
Paircoil
A newer coiled-coil prediction program is Paircoil (Bonnie Berger,
David B. Wilson, Ethan Wolf, Theodore Tonchev, Mari Milla, and Peter S.
Kim, "Predicting Coiled Coils by Use of Pairwise Residue Correlations",
Proceedings
of the National Academy of Science USA, vol 92, Aug 1995,
pp. 8259-8263.) which is available from the MIT
Laboratory of Computer Science. (At present only for UNIX). The new
algorithm is somewhat more stringent than the original Lupas one.
A recent extension to the Paircoil algorithm is Multicoil (MultiCoil:
A program for predicting two- and three-stranded coiled coils. Ethan Wolf,
Peter S. Kim, and Bonnie Berger, Protein Science (1997), 6: 1179-1189).
Hard-boiled
coiled coils Coiled Coils at Sussex University School of Biological Sciences.
Including SOCKET,
a program for analysing coiled coils in protein structures and the CC+
database of coiled coil structures.
