/multicom

The MULTICOM protein structure system. This repository include the source code and documents of both template-based and template-free modeling of the MULTICOM protein structure prediction system. 1D feature prediction, contact prediction, and clustering-based model ranking programs are also included.

Primary LanguagePerl

multicom

updating

(1) Download MULTICOM package (short path is recommended)

cd /home/MULTICOM_TS
git clone https://github.com/multicom-toolbox/multicom
cd multicom

(2) Download the database (required)

wget MULTICOM_db_tools.tar.gz (contact us)

(3) Configure MULTICOM system (required)

a. edit configure.pl

b. set the path of variable '$multicom_db_tools_dir' for multicom databases and tools (i.e., /home/MULTICOM_db_tools/).

c. save configure.pl

perl configure.pl

(4) Mannally configure tools (required)

cd installation/MULTICOM_manually_install_files

# one-time installation. If the path is same as before, the configurations can be skipped.


$ sh ./P1_install_boost.sh 
(** may take ~20 min)

$ sh ./P2_install_OpenBlas.sh 
(** take ~1 min)

$ sh ./P3_install_freecontact.sh 
(** take ~1 min)

$ sh ./P4_install_scwrl4.sh 
(** take ~1 min, after running this shell file, the installation path for scwrl will be reported in the second line. 
Please copy the provided path for scwrl installation)

$ sh ./P5_python_virtual.sh 
(** take ~1 min)

(5) Testing the MULTICOM tools (recommended)

cd installation/MULTICOM_test_codes

ls

sh T1-run-pspro2.sh

sh T2-run-SCRATCH.sh

sh T4-run-dncon2.sh 

sh T5-run-modeller9.16.sh

sh T7-run-hhsearch.sh

sh T11-run-hhsuite.sh

sh T14-run-psiblast.sh

sh T15-run-compass.sh

sh T17-run-prc.sh

sh T20-run-raptorx.sh

sh T27-run-confold.sh

sh T28-run-unicon3d.sh


(6) Run MULTICOM for structure predicton

   Usage:
   $ sh bin/run_multicom.sh <file name>.fasta  <output folder>

   Example:
   $ sh bin/run_multicom.sh examples/T0993s2.fasta test_out/T0993s2_out