Paircoil2
Computation and Biology Group
Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology

http://paircoil2.csail.mit.edu

To install:
Place the configuration file .paircoil2 in your home directory and the 
executable and data files (*.tb) in the directory you will run Paircoil2 in.

To run:
paircoil2 [-win 21|28] fasta_file output_file
where -win specifies a minimum window length (28 is the default), fasta_file
is a file containing one or more fasta-formatted sequence, and output_file will
hold Paircoil2 output.

Please cite:
A. V. McDonnell, T. Jiang, A. E. Keating and B. Berger. 2005. "Paircoil2: 
improved prediction of coiled coils from sequence".  Bioinformatics.

For more information on the Paircoil algorithm, see
"Predicting Coiled Coils by Use of Pairwise Residue Correlations", (Bonnie 
Berger, David B. Wilson, Ethan Wolf, Theodore Tonchev, Maria Milla, and Peter 
S. Kim), PNAS USA (1995) 92: 8259-8263
