I am working with a protein whose structure is not available in PDB, and I wanted to know if it is possible to find the protein residues which are RNA binding.
If the 3D structure of the protein is not available in the Protein Data Bank (PDB), it can be challenging to predict the RNA binding residues accurately. However, there are several methods that can be used to predict the RNA binding residues in the absence of the protein structure:
Sequence-based methods
Homology modeling
Molecular docking
Experimental methods
Also, there are several webservers available that can predict RNA binding sites in a protein sequence. Some of the popular webservers are:
RBRIdent (https://webs.iiitd.edu.in/raghava/rbrident/): RBRIdent is a web server developed by the Indian Institute of Information Technology Delhi that predicts RNA binding residues in a protein using machine learning-based methods.
PRBR (http://sysbio.rnet.missouri.edu/prbr/): PRBR is a web server developed by the University of Missouri that uses evolutionary information and physicochemical properties to predict RNA binding residues in a protein.
RBscore (https://rbscore.cs.uni-potsdam.de/): RBscore is a web server developed by the University of Potsdam that uses structural and sequence-based features to predict RNA binding residues in a protein.
It is important to note that these tools provide predictions based on computational algorithms, and the accuracy of the predictions may vary depending on the protein and the available data.