MSA Depth

MSA depth and cross-chain contacts

¶Although AlphaFold has a high accuracy across the vast majority of deposited PDB structures, we note that there are still factors that affect accuracy or limit the applicability of the model. The model uses MSAs and the accuracy decreases substantially when the median alignment depth is less than around 30 sequences (see Fig. 5a for details). We observe a threshold effect where improvements in MSA depth over around 100 sequences lead to small gains. We hypothesize that the MSA information is needed to coarsely find the correct structure within the early stages of the network, but refinement of that prediction into a high-accuracy model does not depend crucially on the MSA information. The other substantial limitation that we have observed is that AlphaFold is much weaker for proteins that have few intra-chain or homotypic contacts compared to the number of heterotypic contacts (further details are provided in a companion paper39). This typically occurs for bridging domains within larger complexes in which the shape of the protein is created almost entirely by interactions with other chains in the complex. Conversely, AlphaFold is often able to give high-accuracy predictions for homomers, even when the chains are substantially intertwined (Fig. 5b). We expect that the ideas of AlphaFold are readily applicable to predicting full hetero-complexes in a future system and that this will remove the difficulty with protein chains that have a large number of hetero-contacts.

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¶a, Backbone accuracy (lDDT-Cα) for the redundancy-reduced set of the PDB after our training data cut-off, restricting to proteins in which at most 25% of the long-range contacts are between different heteromer chains. We further consider two groups of proteins based on template coverage at 30% sequence identity: covering more than 60% of the chain (n = 6,743 protein chains) and covering less than 30% of the chain (n = 1,596 protein chains). MSA depth is computed by counting the number of non-gap residues for each position in the MSA (using the Neff weighting scheme; see Methods for details) and taking the median across residues. The curves are obtained through Gaussian kernel average smoothing (window size is 0.2 units in log10(Neff)); the shaded area is the 95% confidence interval estimated using bootstrap of 10,000 samples. b, An intertwined homotrimer (PDB 6SK0) is correctly predicted without input stoichiometry and only a weak template (blue is predicted and green is experimental).