The Application of Distributed Computing to the Investigation of Protein Conformational Change

Distributed computing is a potentially very powerfu l approach for accessing large amounts of computational power. Under the umbrella of the comb-e-chem project we have examined distributed computing software and applied it to th e problem of investigating protein conformational change. These investigations require d the development of protein simulations that were suited to distributed computing. Each simulatio n was split into many coupled, parallel parts. These proved challenging to schedule on the flexible and unreliable distributed computing resource. Scheduling algorithms were thus written that identi fied which parts of the simulation were likely to impact the overall efficiency. These parts were then rescheduled to be 'caught-up' via a fast and dedicated cluster.