This repository contains codes for the following work: Peng Xiong, Ruibo Wu, Jian Zhan and Yaoqi Zhou, Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential.
This is free software for non-commercial users. If you have any questions, please contact Peng Xiong via email [email protected]
Make sure these following prerequisites have been installed:
- C++ compiler: Needs to be C++11 compatible. Gcc 9.3.0 and Clang 9.1.0 tested.
- GNU Make
- Git
- CMake
- Wget and Tar - Optional: to download and extract the preprocessed data.
- Clone from the repository:
git clone https://github.com/Jian-Zhan/RNA-BRiQ RNA-BRiQ
- Change directory to
RNA-BRiQ/build/and compile the codes:
mkdir RNA-BRiQ/build/
cd RNA-BRiQ/build/
cmake ../
make
Preprocessed data for the RNA-BRiQ can be downloaded from http://servers.sparks-lab.org/downloads/RNA-BRiQ-data.tar.gz. The data should be downloaded, and extracted to $BRiQ_DATAPATH before continuing.
wget http://servers.sparks-lab.org/downloads/RNA-BRiQ-data.tar.gz
export BRiQ_DATAPATH=FILEPATH/BRiQ_data ## Change "FILEPATH" to the real path to contain the preprocessed data
tar -xvz RNA-BRiQ-data.tar.gz --one-top-level=$BRiQ_DATAPATH
The path containing BRiQ executables should be appended to $PATH. And $BRiQ_DATAPATH should be correctly set.
export BRiQ_DATAPATH=FILEPATH/BRiQ_data ## Change "FILEPATH" to the real path containing the preprocessed data
export PATH=$PATH:FILEPATH/BRiQ/build/bin ## Change "FILEPATH" to the real path containing the compiled codes
Before running the program, you need to prepare the input file. An example files can be found at demo/gcaa/input
pdb gcaa.pdb ## Initial structure in PDB format
seq GCGCAAGC ## RNA nucleotide sequence
sec ((....)) ## Watson-Crick pairs
nwc ..(..).. ## Non-Watson-Crick pairs
fixed 0 1 6 7 ## Index of the fixed nucleotides during structure sampling, starting from 0
If there is only RNA sequence but no reference PDB structure, BRiQ_InitPDB can generate an initial PDB structure from sequence. For example, the following command generates an initial PDB structure for RNA sequence GCGCAAGC.
BRiQ_InitPDB GCGCAAGC init.pdb
And the base pairing information can be extracted by BRiQ_AssignSS from the input PDB structure $INPUTPDB and stored to $OUTFILE:
BRiQ_AssignSS $INPUTPDB $OUTFILE
BRiQ_Refinement is the program to refine the initial structure of a RNA.
BRiQ_Refinement $INPUT $OUTPDB $RANDOMSEED
Where $INPUT is the input file, $OUTPDB is the output structure, and $RANDOMSEED is the random seed.
BRiQ_Predict is the program to predict the structure of a RNA.
BRiQ_Predict $INPUT $OUTPDB $RANDOMSEED
Where $INPUT is the input file, $OUTPDB is the output structure, and $RANDOMSEED is the random seed.
- demo/refinement/: RNA structure refinement.
- demo/partial_predict/: RNA structure prediction from an initial reference structure.
- demo/predict_from_seq_SS/: RNA structure prediction from sequence and pre-assigned secondary structure information.