3dRPC Supplementary Material

About 3dRPC

Three-dimensional structures of complexes of non-coding RNAs with other biomolecules are urgently needed to understand their diverse newly discovered functions. However, the number of them is very limited at present due to difficulties in experimental measure. To solve this problem, computational prediction is another possible approach.For RNA-protein complexes, some protocolshave been proposed for the prediction of the three-dimensional structures, though with parts of algorithms borrowed directly from those of protein-protein complexes only achieved unsatisfying accuracy as the features of RNA-protein interfaces aresignificantly different from those of protein-protein interface. Therefore, we provide a novel computational protocol for RNA-protein complex structure prediction, which adapts new schemes to discrete molecule and charge and to build reference state in order to include specific features of RNA-protein interface. Benchmark shows that this protocol can achieve a high accuracy comparable to current well-developed algorithms for three-dimensional structure prediction of protein-protein complexes.

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You can download 3dRPC to your local machine and run it locally. Please follow the installation guide to install it properly:

  1. Download 3dRPC package from here
  2. Set running environment for 3dRPC. Add the following lines to your “~/.bashrc”:
    export HOME_3dRPC=/home/XXX/3dRPC/
    export X3DNA=${HOME_3dRPC}/ext/X3DNA/
    export PATH=$PATH:${HOME_3dRPC}/ext/fasta/
    source ~/.bashrc
  3. Download and install libraries. Three external libraries are required by 3dRPC: FFTW, BLAS, and LAPACK. The default path of libraries is ${HOME_3dRPC}/lib/.
  4. Install FASTA. FASTA is used for sequence alignment in 3dRPC. The source code of FASTA is located on ${HOME_3dRPC}/ext/fasta/. Users can execute the following command lines to install FASTA:
    cd ${HOME_3dRPC}/ext/fasta/
    After successful installation, an executable file “fasta35” can be found in ${HOME_3dRPC}/ext/fasta/.
  5. Install 3dRPC program from the source code. Run the following command lines given below:
    cd ${HOME_3dRPC}/source
  6. You can read the guide for 3dRPC here.
  7. The data sets can be downloaded here.