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

Description/Abstract

Distributed computing is a potentially very powerful 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 the problem of investigating protein
conformational change. These investigations required the development of protein simulations that
were suited to distributed computing. Each simulation 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 identified 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.