The predicted protein-small molecule structure exhibits numerous clashes

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The predicted protein-small molecule structure exhibits numerous clashes #96

Open gky2023 opened 2 months ago

gky2023 commented 2 months ago

The protein-small molecule complex generated by RFAA has numerous clashes, and even after energy minimization with Schrodinger, there are still many clashes. Does this mean that the resulting structure is not very ideal?

r-krishna commented 2 months ago

There are cases with clashes (see Fig S5C), but usually those also have low predicted confidence