This is a bioinformatics tool to use SAXS data to assemble protein domain structures into full-length structural models
Installation (tested on CentOS Linux 7 (Core))
(1) Setup libraries (required)
Updating
perl setup_env.pl
if report error as "Can't locate Env.pm in @INC (you may need to install the Env module)"
sudo dnf install perl-Env
(2) Configure MULTICOM system (required)
perl configure.pl
(3) Compile SAXSDom from source code (required)
sh compile_SAXSDom.sh
#### output
- Boost version: 1.55.0
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- serialization
-- program_options
-- thread
-- CMAKE_CXX_FLAGS:
running /data/jh7x3/SAXSDom/db_tools/tools/cmake-2.8.12.2/bin/cmake -E create_symlink "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" 2>&1
-- Configuring done
-- Generating done
-- Build files have been written to: /data/jh7x3/SAXSDom/installation/Mocapy++-1.07
Scanning dependencies of target Mocapy
[ 1%] Building CXX object src/CMakeFiles/Mocapy.dir/utils/LogFactorial.cpp.o
[ 2%] Building CXX object src/CMakeFiles/Mocapy.dir/multinomial/MultinomialDensities.cpp.o
[ 3%] Building CXX object src/CMakeFiles/Mocapy.dir/multinomial/MultinomialDensity.cpp.o
[ 4%] Building CXX object src/CMakeFiles/Mocapy.dir/multinomial/MultinomialESS.cpp.o
[ 6%] Building CXX object src/CMakeFiles/Mocapy.dir/dirichlet/DirichletDensities.cpp.o
[ 7%] Building CXX object src/CMakeFiles/Mocapy.dir/dirichlet/DirichletDensity.cpp.o
[ 8%] Building CXX object src/CMakeFiles/Mocapy.dir/dirichlet/DirichletESS.cpp.o
[ 9%] Building CXX object src/CMakeFiles/Mocapy.dir/inference/abstractinfengine.cpp.o
[ 10%] Building CXX object src/CMakeFiles/Mocapy.dir/framework/dbn.cpp.o
...
...
...
Linking CXX static library ../libs/libMocapy.a
[ 96%] Built target Mocapy
Scanning dependencies of target SAXSDom
[ 97%] Building CXX object examples/CMakeFiles/SAXSDom.dir/SAXSDom.cpp.o
Linking CXX executable SAXSDom
[ 97%] Built target SAXSDom
Scanning dependencies of target mdarray
[ 98%] Building CXX object examples/CMakeFiles/mdarray.dir/mdarray.cpp.o
Linking CXX executable mdarray
[ 98%] Built target mdarray
Scanning dependencies of target mlr-uni
[100%] Building CXX object examples/CMakeFiles/mlr-uni.dir/mlr-uni.cpp.o
Linking CXX executable mlr-uni
[100%] Built target mlr-uni
Example I
cd examples
sh T1-run-3p02A.sh
#### output:
All running jobs are done
Ranking score for models can be found at /data/jh7x3/SAXSDom/test_out/3p02A_test//all_models_qprob/3p02A.Qprob_score
Best model: /data/jh7x3/SAXSDom/test_out/3p02A_test//3p02A_SAXSDom_top1.pdb
Structure1: ./3p02A_SA Length= 305
Structure2: ../../exam Length= 305 (by which all scores are normalized)
Number of residues in common= 305
RMSD of the common residues= 5.987
TM-score = 0.6475 (d0= 6.41, TM10= 0.6060)
MaxSub-score= 0.4714 (d0= 3.50)
GDT-TS-score= 0.5795 %(d<1)=0.4557 %(d<2)=0.4754 %(d<4)=0.5377 %(d<8)=0.8492
GDT-HA-score= 0.4738 %(d<0.5)=0.4262 %(d<1)=0.4557 %(d<2)=0.4754 %(d<4)=0.5377
Example II
cd examples
sh T1-run-SASDBJ3.sh
### Output:
Best model: /data/jh7x3/SAXSDom/test_out/SASDBJ3_test/SASDBJ3_SAXSDom_top1.pdb
Evaluating the model
*****************************************************************************
* TM-SCORE *
* A scoring function to assess the quality of protein structure predictions *
* Based on statistics: *
* 0.0 < TM-score < 0.17, Random predictions *
* 0.4 < TM-score < 1.00, Meaningful predictions *
* Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 *
* For comments, please email to: yzhang@ku.edu *
*****************************************************************************
Structure1: /data/jh7x Length= 583
Structure2: /data/jh7x Length= 583 (by which all scores are normalized)
Number of residues in common= 583
RMSD of the common residues= 6.162
TM-score = 0.7032 (d0= 8.47, TM10= 0.6815)
MaxSub-score= 0.4868 (d0= 3.50)
GDT-TS-score= 0.5836 %(d<1)=0.4700 %(d<2)=0.5026 %(d<4)=0.5369 %(d<8)=0.8250
GDT-HA-score= 0.4271 %(d<0.5)=0.1990 %(d<1)=0.4700 %(d<2)=0.5026 %(d<4)=0.5369
Example III
cd examples
sh T1-run-RcPutA.sh
(4) Run SAXSDom
Usage:
sh bin/run_SAXSDom.sh <target id> <fasta file> <saxs file> <domain list with path> <output directory> <number of cores to run, default:1>
Example I:
sh bin/run_SAXSDom.sh 3p02A examples/3p02A/3p02A.fasta examples/3p02A/saxs_profile.dat examples/3p02A/domain_list_withPath_reindex test_out/3p02A 5
Example II:
sh bin/run_SAXSDom.sh SASDBJ3 examples/SASDBJ3/SASDBJ3.fasta examples/SASDBJ3/SASDBJ3-A.dat examples/SASDBJ3/domain_list_withPath_reindex test_out/SASDBJ3_benchmark 5
Example III:
sh bin/run_SAXSDom.sh RcPutA examples/RcPutA/RcPutA_full.fasta examples/RcPutA/RcH7m23.dat examples/RcPutA/domain_list_withPath_reindex test_out/RcPutA 5
(5) Run SAXSDom-abinitio
Usage:
sh bin/run_SAXSDom_abinitio.sh <target id> <fasta file> <domain list with path> <output directory> <number of cores to run, default:1>
Example I:
sh bin/run_SAXSDom_abinitio.sh 3p02A examples/3p02A/3p02A.fasta examples/3p02A/domain_list_withPath_reindex test_out/3p02A_abinitio 5
Example II:
sh bin/run_SAXSDom_abinitio.sh SASDBJ3 examples/SASDBJ3/SASDBJ3.fasta examples/SASDBJ3/domain_list_withPath_reindex test_out/SASDBJ3_abinitio 5
Example III:
sh bin/run_SAXSDom_abinitio.sh RcPutA examples/RcPutA/RcPutA_full.fasta examples/RcPutA/domain_list_withPath_reindex test_out/RcPutA_abinitio 5