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C-RCPred: Constrained RNA Complex Prediction

C-RCPred is an open-source bioinformatics program for the prediction of RNA complexes.
The multi-objective algorithm is implemented in C++ and runs on UNIX-like operating systems.

Besides this stand-alone version, a web server is also available on the EvryRNA platform: click here.


If all the dependencies are already installed on your system, a simple make within the C-RCPred directory is sufficient to build the executable file.
Alternatively, C-RCPred can easily be installed by using Docker as follows:

git clone
cd C-RCPred
docker build -t c-rcpred ./

The above command has been tested with Docker version 20.10.7.


The installation of C-RCPred depends on two bioinformatics libraries:

  • the ViennaRNA package (version 2.5.1)
  • the NUPACK software suite (version 3.2.2)

The CPLEX Optimizer (version 22.10) is also required.

In the Dockerfile, you can find the other dependencies that can be installed with your Linux package manager.


Two sets of files are provided to test C-RCPred. Each set contains 4 input files (.fasta, .txt30, .txt90, and .txt).
An example of command is:

./C-RCPred -f test/NDB_00016.fasta \
           -s test/NDB_00016_str.txt30 \
           -i test/NDB_00016_inter.txt90 \
           -p test/NDB_00016_probing.txt \
           -l 20 -u 80 -t 100 -e 1 \
           -g NDB_00016_graph.txt \
           -q NDB_00016_cliques.txt -m 20

Here, the results are written in the NDB_00016_graph.txt and NDB_00016_cliques.txt files, in addition to the terminal output.

The same test can be performed with the files provided for PDB_00805.


The following list of options can also be accessed by running ./C-RCPred:

 -f:       input fasta file
 -s:       input secondary structure files,
 -i:       input interaction secondary structure files,
 -c:       constraint files where constraints are in the same order than the secondary structure and interaction files
 -p:       probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)
 -o:       format of output "d" (dot-parenthesis, default), "j" (json) or "b" (base pair list format)
 -e:       energy model (0: No energy model (use energies computed by upstream tools)), (1: ViennaRNA package model, default), (2: NUPACK model)
 -t:       threshold for compatibility RNA (0->100, default 100)
 -l:       lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)
 -u:       upper probing threshold  (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)
 -g:       output graph file
 -k:       output cliques predicted
 -q:       output cliques predicted without duplicates
 -m:       maximum number of structures to output