Savas, B.; Yilmazbilek, I.; Ozsan, A.; Karaca, E.

In the 55th round of CAPRI, we primarily used enhanced AlphaFold2 (AF2) sampling and data-driven docking. Our AF2 protocol relies on Wallner\'s aggressive sampling approach, which combines different AF2 versions and sampling parameters to produce thousands of models per target. For T231 (an antibody peptide complex) and T232 (PP2A:TIPRL complex), we employed a 50-fold reduced mini aggressive sampling and a custom ranking approach, leading to a top-ranking medium prediction in both cases. In the cases of T233 and T234 (two antibody bound MHC I complexes), we followed data-driven docking, which did not lead to an acceptable solution. Our post-CAPRI55 analysis showed that if we would have used our mini aggressive sampling on T233 and T234, we could have submitted a medium-quality model for T233 as well. For the scoring challenge, we utilized the scoring function of FoldX, which was effective in selecting acceptable models for T231 and medium quality models for T232. Our success, especially in predicting and ranking a medium quality model in the case of antibody-peptide T231 underscores the feasibility of greener and accurate enhanced AF2 sampling. It also highlights the ongoing need for alternative ranking approaches for antibody complexes.