Bujnicki lab - ClaPNAC

ClaPNAC: a Classifier of Protein – Nucleic Acid Contacts 

 

Program Summary:

 

ClaPNAC is a classifier that annotates 3D structures of nucleic acid–protein complexes with pairwise contacts. It distinguishes stacking interactions (involving the faces of nucleobases), pseudo pairs (involving the Watson-Crick, Hoogsteen, or sugar edge of the base), and phosphate and ribose interactions on the nucleoside/nucleotide side, as well as sidechain and backbone interactions on the amino acid side. ClaPNAC is based on a geometric approach, extending our previous method ClaRNA, and uses a database of pre-classified doublets extracted from experimentally solved RNA–protein complex structures.  
Current version: 
The current version is 1.00. 

 

Availability: 

ClaPNAC is an open-source tool.
Program's download location: https://doi.org/10.5281/zenodo.15423174
 
User Manual

 

Chosen representatives of each class could be found in ./classes_PDB
As a result you will see the score from 0 to 1 for each class.
NA_id P_id score type N-AA
B-203   A-4     0.63    P       A-GLY

 

Side libraries

 

python 3.8
ClaPNAC requiers numpyargparsepandasseabornmatplotlibalive_progress.

 

Usage

 

Takes all files in .pdb or .cif from input directory and annotate N-AA contacts. The results are saving into csv files. ([inputfile][representation][threshold].csv)
-i input directory
-t full atom (FA) or coarse-grained (CGR) representation will be used
-o threshold for output scores, doublets esimated with the score lower than threshold will be not included in the report file
-r is a range number for ContExt, means the maximum distance for the contacts.
-s option is for sequence: it shows sequence and mark * residues making interactions with score > 0.5
Please see the examples in test directory
python -h python -i [input directory] -t [FA or CGR] -o [float number] -r [float number] -s

 

Citations: 

https://doi.org/10.1101/2025.05.30.657037

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