IIT Madras

PDA-Pred

Protein-DNA complex Binding Affinity Prediction		 Protein Bioinformatics Lab

Tutorial


The predict page can be accessed from here.

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

Input options:

  1. The page has option to enter PDB ID of protein-DNA 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 DNA. Multiple chain Ids can be entered with comma. (Optional)
  4. User should select one of the DNA class for the prediction. *
    • single strand
    • Double strand
  5. User should select one of the strucutral class of protein for the prediction, if the DNA is double stranded *
    • all-α
    • all-β
    • αβ
    • others
  6. User should select one of the Functional class of protein for the prediction. *
    • Regulatory
    • other (non-regulatory)
  7. Any problem with the server: Users can download source code from: https://github.com/Harinikannan98/PDA-PreD
* Mandatory fields.

Example 1:

Crystal Structure of UP1 Complexed With DNA

Input:

PDB ID: 1po6, belongs to 'single strand DNA' classification.

Example 1 1po6

Result for example 1:

Example 1 1po6

Example 2:

HIN RECOMBINASE BOUND TO DNA

Input:

PDB ID: 1hcr, Protein chain ID: A, DNA Chain ID: B,C, belongs to 'ds-All Alpha-non-regulatory' classification.

Example 2 1hcr

Result for example 2:

Example 2 1hcr

Example 3:

Complex of human alpha thrombin with DNA aptamer

Input: PDB: 6z8x,belongs to 'ds-Alpha-beta-non-regulatory'

.

Example 3 6z8x

Result for example 3:

Example 3 6z8x