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JeffSHF / ColabDock

Code for ColabDock paper
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restrains specification in Colab Dock notebook #4

Open biotech70 opened 1 year ago

biotech70 commented 1 year ago

I have a fundamental inquiry: Where and how can we restrains for the target template? Do we need to perform a global docking using tools like ColabFold or AlphaFold and then use the resulting output in the restraint section, or are there other methods available?

JeffSHF commented 1 year ago

Hi, there. Colabdock is only suitable for docking proteins when you have experimental restraints, such as restraints derived from NMR, covalent labeling, DMS. If there is no such restraints, you should use AF2 (AF-multimer) directly, or other popular docking methods.