Protein-RNA binding affinity prediction This program takes the input of protein-DNA complex and predicts the binding affinity.
Input options: User can input PDB ID of protein-RNA complex or can provide the file in PDB format. User can enter the chain ID of protein. Multiple chain Ids can be entered with comma. (Eg. Chain ID: A,B) (Optional) User can enter the chain ID of RNA. Multiple chain Ids can be entered with comma. (Optional) User should select one of the RNA class for the prediction.
User should select one of the Functional class of protein for the prediction. *
Dependencies:
Program is basically using python3, and demands few python packages to run. Please ensure the packages such os,re, Bio, numpy, functools,sys, time, shutil, subprocess, math, uuid, cgitb, timeit, wget, glob, urllib, pandas, warnings are installed. Make sure to edit the naccess executable file with the path of local installation (Source: http://www.bioinf.manchester.ac.uk/naccess/). Also needs the installation of 3vvv software, used for volume and surface area calculation (Source: https://github.com/vosslab/vossvolvox) Kindly install the Foldx software. (Source: https://foldxsuite.crg.eu/) Execute x3dna_setup and add the path to environment variable (http://forum.x3dna.org/downloads/3dna-download/). Request and download the 3DNA. Run:
Run "python3 pdpredict.py" Enter option for PDB-ID and PDB-file Provide the PDB ID or PDB-file with chain Enter the RNA strand and functional class The program will be executed, and the result will be provided in result.txt In the Form of PDB ID, Chain, Predicted affinity(kcal/mol), dissocation constant(M). You can also access it through the webserver https://web.iitm.ac.in/bioinfo2/prapred/index.html