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.
Web service: http://sysbio.rnet.missouri.edu/multicom_cluster/
(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)
***one-time installation. If the path is same as before, the configurations can be skipped.
cd installation/MULTICOM_manually_install_files
$ 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) Set theano as backend for keras (required)
Change the contents in '~/.keras/keras.json'. DNCON2 is currently running based on theano-compiled models.
$ vi ~/.keras/keras.json
{
"epsilon": 1e-07,
"floatx": "float32",
"image_data_format": "channels_last",
"backend": "theano"
}
(6) Testing the individual tools in MULTICOM (recommended)
cd installation/MULTICOM_test_codes
a. Sequential testing
perl test_multicom_all_parallel.pl
b. Parallel tesing up to 5 jobs at same time
perl test_multicom_all_parallel.pl 5
(7) Validate the individual predictons
cd installation/MULTICOM_test_codes
sh T99-run-validation.sh
(8) Testing the integrated MULTICOM system (recommended)
cd examples
sh T0-run-multicom-T1006.sh
sh T0-run-multicom-hard-T0957s2.sh
(9) Run MULTICOM for structure predicton
Usage:
$ sh bin/run_multicom.sh <target id> <file name>.fasta <output folder>
Example:
$ sh bin/run_multicom.sh T0993s2 examples/T0993s2.fasta test_out/T0993s2_out