You are trying to dock two proteins which are modelled. Statistically, the reliability of the result already dropped to 50%. Let me explain in details. In a high resolution X-ray crystal structure one may obtain 100% reliability regarding the positions of the atoms. But a homology model gives a maximum score of around 0.8 (80%). Therefore, the possibility of both the modeled structure being true becomes 0.8*0.8 = 0.64 (assuming that you have managed to obtained the best homology models). Now, even if you manage to obtain the best possible docked structure with a very high reliability of say 80%, the overall reliability of the docked complex becomes 0.64*0.8=0.51.

Dear Mr. Usman,

Visualization of the binding geometries and interactions are mandatory. The binding site analysis is also important. Protein-protein interaction plots might show one of the reliable ways to analyze docking results.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213718/

Thanks.

Best wishes,

Sk. Abdul Amin

You are trying to dock two proteins which are modelled. Statistically, the reliability of the result already dropped to 50%. Let me explain in details. In a high resolution X-ray crystal structure one may obtain 100% reliability regarding the positions of the atoms. But a homology model gives a maximum score of around 0.8 (80%). Therefore, the possibility of both the modeled structure being true becomes 0.8*0.8 = 0.64 (assuming that you have managed to obtained the best homology models). Now, even if you manage to obtain the best possible docked structure with a very high reliability of say 80%, the overall reliability of the docked complex becomes 0.64*0.8=0.51.

Hello,

I use RosettaDock server for docking.

It gives you many parameters.

For the visualization I use UCSF Chimera.

Thank you,

Victor

Thank you All For You Answers .. :)