Hi, we've currently been researching about mutant HIV-1 RT, and we're having a hard time figuring out what software to use in order to determine the protein's binding site (so we wouldn't have to do blind docking, making the results less accurate). We've currently been using the COACH algorithm, but it only detects one chain of the protein (our proteins usually have two chains e.g., 6uk0 has two chains: the p51 and p66 subunits ).

this is the link for the algorithm: https://zhanggroup.org/COACH/