PRA-Pred

The predict page can be accessed from here.

This page takes input of protein-RNA complex and predicts the binding affinity.

Input options:

1. The page has option to enter PDB ID of protein-RNA complex or user can upload their file in PDB format. *
2. User has option to enter the chain ID of protein. Multiple chain Ids can be entered with comma. (Eg. Chain ID: A,B) (Optional)
3. User can enter the chain ID of RNA. Multiple chain Ids can be entered with comma. (Optional)
4. User should select one of the RNA class for the prediction. *
• single strand
• Double strand
5. User should select one of the Functional class of protein for the prediction. *
• Enzyme
• Regulatory
• Others

* Mandatory fields.

Example 1:

Structure of SRSF1 RRM2 in complex with the RNA 5'-UGAAGGAC-3'

Input:

PDB ID: 2m8d, belongs to 'single stranded RNA with regulatory protein' classification.

Result for example 1:

Example 2:

Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor

Input:

PDB ID: 1jbr, belongs to 'Double strand RNA with enzyme protein' classification.

Result for example 2:

Example 3:

RNA recognition by the Vts1 SAM domain

Input: PDB: 2b6g,belongs to 'Double strand RNA with Regulatory protein' classification

.

Result for example 3: