Fig. 2: Comparison of predictions for single chains and complexes.
a, Structure prediction comparison of AlphaFold2, AlphaFold-Colab and ColabFold-AlphaFold2 with BFD/MGnify and with the ColabFoldDB, and ColabFold-RoseTTAFold with BFD/MGnify using predictions of 91 domains of 65 CASP14 targets. The 28 domains from the 20 free-modeling (FM) targets are shown first. FM targets were used to optimize MMseqs2 search parameters. Each target was evaluated for each individual domain (in total 91 domains). b, MSA generation and model inference times for each CASP14 FM target sorted by protein length (same colors as before). Blue shows MSA run times for ColabFold-AlphaFold2-BFD/MGnify and ColabFold-RoseTTAFold-BFD/MGnify. c, Comparison of multimeric prediction modes in ColabFold and AlphaFold-multimer. The ColabFold modes include residue-index modification with models originally trained for single-chain predictions and those for multimeric prediction from AlphaFold-multimer, using DockQ (a quality measure for protein–protein docking models). d, Run time of colabfold_batch proteome prediction at three optimization levels: always recompile, default, and stop model/recycle evaluation after first prediction with a pLDDT of ≥85. The yellow dashed line represents an extrapolation on the basis of the 50 AlphaFold2 predictions.
