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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 freely available on the EvryRNA platform.


If all the dependencies are already installed on your system, using the make command 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 docker build command has been tested for Docker version 20.10.7.


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

The CPLEX Optimizer (version 22.10) is also required.

In the Dockerfile, the other dependencies that must be installed can be found.


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

This command will output predicted secondary structures, represented with the dot-bracket notation.
Other results will be written in the NDB_00016_graph.txt and NDB_00016_cliques.txt files (see options below).

A similar test can be performed with the files provided for PDB_00805.


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

 -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




  1. Lorenz R, Bernhart SH, Höner zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 2011, doi:10.1186/1748-7188-6-26 

  2. Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA. NUPACK: Analysis and design of nucleic acid systems Journal of Computational Chemistry, 2011, doi:10.1002/jcc.21596