Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers

Abstract Understanding the structures of protein complexes is pivotal for breakthroughs in health, agriculture, bioengineering, and beyond. MultiFOLD2 and ModFOLDdock2 are leading servers for protein quaternary structure prediction and model quality assessment, respectively. MultiFOLD2 includes integrated stoichiometry prediction for quaternary structures and improved sampling and scoring, leading to high performance in continuous independent benchmarks such as CAMEO. ModFOLDdock2 uses a hybrid consensus approach to generate global and local quality scores for predicted quaternary structures. ModFOLDdock2 is integrated with MultiFOLD2 while also being available as a stand-alone server, enabling the independent evaluation of quaternary structure models from any source. Both servers have been independently rigorously evaluated, demonstrating high performance and ranking among the top servers in their respective categories in the recent CASP16 experiment. The MultiFOLD2 and ModFOLDdock2 servers are freely accessible through user-friendly web interfaces at https://www.reading.ac.uk/bioinf/.