Help with MSA #277
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When using Chai (including the web version), I encountered an issue where the pTM score of a protein predicted using MSA is lower than that without using MSA. For example, the pTM score with MSA is only 0.72, but the prediction score without selecting the MSA option is 0.90. |
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MSAs do not provide convincing/consistent information with model's expectations. |
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MSAs do not provide convincing/consistent information with model's expectations.
Check that found MSAs are relevant for your example. Specifically, for newly designed proteins, MSAs can be irrelevant as they are not evolutionary connected to the protein you try to fold