Betacon: a software package to predict the beta-sheet topology of a protein
Free for Academic Use Only.
All rights reserved.


Author: 
Dr. Jianlin Cheng
Department of Computer Science
University of Missouri, Columbia
Email: chengji@missouri.edu

Installation:

open configure.pl


set $install_dir to the installation dir of betacon


set $pspro_dir to the installation dir of pspro

save configure.pl


run it "./configure.pl"

Installation is done.

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Two scripts:

(1) beta_contact_map.sh 
	predict both regular contact map and beta-sheet contact map.
	combine them into one map.


	beta_contact_map.sh    fasta_file ouptut_dir


(2) predict_beta_fasta.sh 
	predict the pairing probability matrix of beta sheet residues
	predict_beta_fasta.sh fasta_file  output_file


In output_dir, 

	fasta_file.con8a.csp  (selected contacts at 8A distance threshold in CASP format)

	fasta_file.cm12a    (contact map at 12A using full 2D RNN)
	fasta_file.bcm12a   (contact map at 12A using band RNN)
	fasta_file.cm8a     (contact map at 8A using full 2D RNN)
	fasta_file.bcm8a    (contact map at 8A using band RNN)
	fasta_file.con8a    (combined map at 8A using both full 2D RNN and band RNN)

	fasta_file.cm8a.comb  (8 angstrom contact map combined with beta-sheet pairing map using full 2D RNN)
	fasta_file.bcm8a.comb (8 angstrom contact map combined with beta-sheet pairing map using band 2D RNN)
	fasta_file.cm12a.comb (12 angstrom contact map combined with beta-sheet pairing map)
	fasta_file.con8a.comb (8 angstrom contact map of combining full 2D, band RNN, and beta-sheet pairing)


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