Liu Lab at Huazhong University of Science and Technology








PRIME 2.0.1: A program can be used for prediction protein-DNA complex structure

PRIME 2.0 is used to predict the structure of protein-RNA complexes. Currently, it was updated to PRIME 2.0.1, which can be used to predict the structure of protein-DNA complexes. PRIME 2.0.1 includes TMalign (protein structural alignment) and RMalign(RNA/DNA structural alignment) for searching template in the library. Protein and DNA structure coordinates are needed. The output is the protein-DNA complex structure model. The similar score (TMscore or complex structural score),which describle the binding similarity between the target and the template, and a transformation matrix are also reported.

PRIME 2.0.1 is available.

During developing PRIME 2.0.1, a template library is also collected.
HELP for PRIME 2.0.1 USERS:

1. INSTALLATION:
download PRIME 2.0.1 package.
type "tar zxvf PRIME 2.0.1.tar.gz" to uncompress and unpack the package.
type "cd PRIME 2.0.1" to change the current directory.
type "./INSTALL.sh" to compile the programm.


2. USAGE:
Once PRIME 2.0.1 has been installed in your computer successfully! You can start PRIME 2.0.1 by running this command at the directory "example".
1) build and evaluate the model if the native structure is known:
../source/PRIME -mode 15 -system 4 -par parameter_build_evaluate_model

A model of target(4WLW_A and 4WLW_Y) is built on the template(4WLW_AY) by PRIME 2.0.1. Two files *.trasnsform (transformation matrix) and *tmscore (ligand rmsd comparing with the native ) are generated. Also outputs a model of pdb format.

2) build the model if the native structure is unknown:
../source/PRIME -mode 15 -system 4 -par parameter_build_model

A model of target(1R8D_A and 1R8D_C) is built on the template(4WLW_AY) by PRIME 2.0.1. Just one file *.trasnsform (transformation matrix) is generated because native structure is not assigned.

3) build models with template library:
  3.1 add template library to PRIME 2.0.1:
    1) download the template PDB file
    2) unpack and uncompress the template to one directory(example: ~/template)
    3) change directory to "example" and type ./add_template.sh ~/template NRBC1536
    4) this will generate parameter which includes all 1536 templates
    By the way, any templates can be added with this way.
  3.2 run ../source/PRIME -mode 15 -system 4 -par parameter at example directory
  3.3 check the complex structure score in the file *.transform. According to our research, a good model could be built by PRIME 2.0.1 with the template that complex structural score is greater than 0.45.(See paper for detail).
All parameters are set at the file parameter, see README for detail in the PRIME 2.0.1 package.

if the compiler prompts "g++: /usr/lib64/libgfortran.so.3: No such file or directory", please modify the makefile file so that PRIME 2.0.1 can link to libgfortran(replace "/usr/lib64/libgfortran.so.3" to the real file path in your linux)

if PRIME 2.0.1 prompt the error: Can't find the SARA_normalized_file, please type "source ~/.bashrc" to reload the env.

CONTACT US:
Any questions about PRIME 2.0.1, please email to liushiyong@gmail.com.
Reference:
1. Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser and Shiyong Liu. Template-based modeling of protein-RNA interactions.
PLOS Computational Biology 2016 Sep 23;12(9)[PubMed] [PDF]
2. Jinfang Zheng, Juan Xie, Xu Hong and Shiyong Liu. RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.
BMC Genomics [PubMed][PDF]
3. Juan Xie, Jinfang Zheng, Xu Hong, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu and Shiyong Liu. Protein-DNA complex structure modeling based on structural template.
Biochemical and Biophysical Research Communications [PDF]