I am examining the unknown binding conformation of two protein components (each of which have known/established crystal structures). I have derived a conformation of the two protein components using distance constraints from various cross-linkers. However, I am not sure if the derived structures are energetically possible or favorable. I am not too familiar with how to do molecular modeling/protein docking. Would anyone be able to suggest any free software available for obtaining an energetically possible protein conformation using my cross-linking distance constraints that does not require a great deal of protein docking expertise? Thank you.
The best software to start with will be HADDOCK:
http://haddock.science.uu.nl/
there is an online server (no installation required) and info on how to use it.
It will suit you cause you can input restrains, so your docking will not be random.
Hopefully it will give you good result,
Best of Luck
Please have a look at the following website:
https://www.wenmr.eu/wenmr/generating-necessary-restraint-files-running-haddock-manually
there are a lot of possibilities but you have to try and find what is more suitable for you: it will be fun to learn it.
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