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The apoptosome, a critical protein complex in apoptosis regulation, relies on intricate interactions between its components, particularly the proteins containing the Caspase Activation and Recruitment Domain (CARD). This work presents a thorough computational analysis of the stability and specificity of CARD-CARD interactions within the apoptosome. Departing from available crystal structures, we identify important residues for the interaction between the CARD domains of Apaf-1 and Caspase-9. Our results underscore the essential role of these residues in apoptosome activity, offering prospects for targeted intervention strategies. Available experimental complex structures were able to validate the protein-protein docking consensus approach used herein. We furthermore extended our analysis to explore the specificity of CARD-CARD interactions by cross-docking experiments between apoptosome and PIDDosome components, between which there should not be any interaction despite belonging to the same death fold subfamily. Our findings indicate that native interactions within individual complexes exhibit greater stability than the cross-docked complexes, emphasizing the specificity required for effective protein complex formation. This study enhances our understanding of apoptotic regulation and demonstrates the utility of computational approaches in elucidating intricate protein-protein interactions.