FIGURE 4.

The impact of MSA pairing on prediction accuracy. MSAs were generated using MMseqs2 using the “advanced” interface of ColabFold. ²⁹ Pairing was performed in ColabFold on a total of 17 cases whose ligand and receptor proteins come from the same prokaryotic organism. Cases in the heatmap were sorted by the paired MSA depth (N _eff; see Material and Methods for details) from the largest to the smallest values. Structural predictions were generated with the “advanced” interface of ColabFold, and RoseTTAFold ²⁸ (through the Robetta server). All models were assessed for near‐native predictions within the top‐ranked (T1) and top 5 (T5) models using CAPRI criteria. Complex category: Enzyme‐inhibitor (EI), enzyme complex with a regulatory or accessory chain (ER), enzyme‐substrate (ES), others, receptor‐containing (OR); others, miscellaneous (OX)