Dear Modeller users, I need to model induced protein-ligand fit. Flexibility is supposed to be defined mostly by only one of the loops in the protein, so I probably don’t need to do a molecular dynamics, but can just make simulated annealing and conformational sampling for this loop. Is it possible to do it somehow in parallel with protein docking – for example with ligand present or by any other way to include ligand influence on loop position? But in general looks like the simplest way is to make loop sampling, perform docking and check final complexes by score/analyze manually.

Best regards, Andrew