CONFOLD version 2.0 (CONFOLD2) 7/12/2016
CONFOLD2 is a contact-guided protein structure prediction tool. Most scripts are written in Perl. It takes predicted contacts file (CASP RR format) and 3-state secondary structure (SCRATCH fasta format) as input and delivers top 5 models.
Installing CONFOLD
- Install CNS-suite (see below for instructions).
- Update paths for the variables
$cns_suite
incore.pl
. - Configure how CONFOLD2 will be parallelized.
Current (default) configuration is to use HPC cluster.
Make appropriate changes at lines 113-117 of
confold2-main.pl
to run in a local machine. - Test the program:
$ ./confold2-main.pl -rr ./dry-run/input/1guu.rr -ss ./dry-run/input/1guu.ss -out ./output-1guu
Installing CNS Suite
- To download CNS suite, provide your academic profile related
information at http://cns-online.org/cns_request/. An email
with (a) link to download, (b) login, and (c) password
will be sent to you. Follow the link, possibly
http://cns-online.org/download/, and download
CNS suite
cns_solve_1.3_all_intel-mac_linux.tar.gz
. - Unzip
$ tar xzvf cns_solve_1.3_all_intel-mac_linux.tar.gz
- Change directory to cns_solve
$ cd cns_solve_1.3
- Unhide the file
.cns_solve_env_sh
$ mv .cns_solve_env_sh cns_solve_env.sh
- Edit (a)
cns_solve_env.sh
and (b)cns_solve_env
to replace_CNSsolve_location_
with CNS installation directory. For instance, if your CNS installation path is/home/user/programs/cns_solve_1.3
replace_CNSsolve_location_
with this path - Test CNS installation
$ source cns_solve_env.sh
$ cd test
$ ../bin/run_tests -tidy *.inp
Predictions for PSICOV, CASP11, and CASP12 datasets
The contact predictions, secondary structure predictions, and CONFOLD2 reconstructed models for (a) PSICOV dataset using PSICOV contacts, (b) PSICOV dataset using MetaPSICOV contacts, (c) CASP11 dataset using CONSIP2 contacts, and (d) CASP12 dataset using RaptorX contacts are available at http://sysbio.rnet.missouri.edu/bdm_download/confold2/.
Contact
bap54@mail.missouri.edu (developer) chengji@missouri.edu (PI)