ADL: Question about docking molecules alongside an endogenous ligand (Vina)

Van Dam, Hubertus hvandam at
Mon Aug 17 10:57:25 PDT 2020

Hi Matt,

Docking codes are generally not designed to predict poses in a such a system. However, that does not mean that you cannot do it. I have actually done this once (accidentally, when I was given a protein structure that contained a ligand by mistake) and so yes you can dock to that. However, you would have to think about what the results mean.

Best wishes,


Hubertus van Dam, 631-344-6020, hvandam at
Brookhaven National Laboratory

On 8/14/20, 23:25, "autodock-bounces at on behalf of Matt K." <autodock-bounces at on behalf of 5xx7xx at> wrote:

    I have a protein with an endogenous ligand which is so highly abundant that
    I have little chances of outperforming it with a drug. Can I leave it in
    place and dock other molecules next to it with Vina? Or is the software not
    designed to predict poses in such a system?
    --- ADL: AutoDock List  ---;!!P4SdNyxKAPE!S7EtMudpGHvwzdDyO38OCQSi0cAJ6184WQZJk3ZY_N2ge57hEk4rOTSVaHmKGsU$  ---

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