Rajeshwari Ganapathy : You could use AlphaFold2. Please note that AlphaFold3 could be even better, but the user policy for AlphaFord3 currently does not allow its use for predicting structures that would be employed subsequently as docking targets.

Try using AI tools like Rudy J Richardson has mentioned.

Apart from AlphaFold use can use RoseTTAFold also.

Since you have mentioned poor binding affinity with known drug, try doing site directed docking.

You can also cross check your results with other docking engines.

Regards.

To improve your protein structure prediction for molecular docking studies:

Finally, consider optimizing the docking protocol, including receptor flexibility (by including conformational sampling or using flexible docking methods).

The best way to predict a protein's 3D structure is by combining multiple methods and refining the model. You can refine your predicted structures using molecular dynamics simulations and structural optimization. Also, consider using homology modeling with a high sequence identity template or experiment-based methods if available.

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.