PxR3D-map - Structural-based prediction of protein-RNA photo-crosslinking sites

PxR3D includes two parts: protein-RNA 3D structural feature extraction and crosslinking site prediction.

Installation & prerequisites

• czplib

Download and install the czplib perl library files: https://github.com/chaolinzhanglab/czplib

• 3DNA

Please refer to https://x3dna.org for installation details.

• R packages

The two R scripts depend on various functions wrapped in utils.R with a list of dependent R packages such as Caret for random foreast prediction. Please install these packages first before running the codes below.

Structural feature extraction

Protein-RNA structural feature extraction mainly uses 3dna2matrix_wrapper.pl, which depends on DSSR and SNAP of the 3DNA tookit.

When running 3dna2matirx_wrapper.pl, specify the directory of 3DNA 'e.g., ~/tools/3dna'.

The script requires PDB accession number as input and outputs the features related to amino acids and RNAs in the complex structure.

3dna2matrix_wrapper.pl [options] --3dna ~/tools/3dna <in.pdb> <out.rna.txt> <out.aa.txt>

The output files 'out.rna.txt' and 'out.aa.txt' are used to build the feature matrix. The crosslinking status of each nucleotide or amino acid needs to be added to train the models for prediction. See examples/featuretable.nt.txt and examples/featuretable.aa.txt.

Crosslinking site prediction

After extracting the structural features, PxR3D adopts Random Forest to predict crosslinking nucleotides by PxR3D_nt.R and crosslinking amino acids by PxR3D_aa.R .

Prediction of crosslinking nucleotides

Rscript PxR3D_nt.R -v -f test.nt.plot.pdf -i example/featuretable.nt.txt -o test.nt.model.Rds

Prediction of crosslinking amino acids

Rscript PxR3D_aa.R -v -f test.aa.plot.pdf -i example/featuretable.aa.txt -o test.aa.model.Rds

Please refer to example folder for the input format.

Citation

H Feng, XJ Lu, L Liu, D Ustianenko, C Zhang. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. bioRxiv, 2022.06. 02.494568