Improved ab initio protein structure reconstruction
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confold-v2.0
LICENSE
README.md
confold-v2.0.zip

README.md


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

  1. Install CNS-suite (see below for instructions).
  2. Update paths for the variables '$cns_suite' in 'core.pl'.
  3. 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.
  4. Test the program: $ ./confold2-main.pl -rr ./dry-run/input/1guu.rr -ss ./dry-run/input/1guu.ss -out ./output-1guu

Installing CNS Suite

  1. 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".
  2. Unzip $ tar xzvf cns_solve_1.3_all_intel-mac_linux.tar.gz
  3. Change directory to cns_solve $ cd cns_solve_1.3
  4. Unhide the file '.cns_solve_env_sh' $ mv .cns_solve_env_sh cns_solve_env.sh
  5. 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
  6. 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)