Mapping conformational pathways between known functional protein states

Understanding and elucidating the conformational rearrangements that protein systems undergo to transition between different functional states is an important but challenging problem in computational biology [1]. Wet-lab techniques allow resolving representative structures of a protein's functional states but rarely provide the microscopic picture of transition trajectories connecting these states. While computational methods based on Molecular Dynamics in principle offer to incorporate dynamics and obtain transition trajectories, the computational complexity of the problem results in impractical running times. Foregoing dynamics allows computing conformational paths in an efficient manner. MD-based techniques can be employed to map conformational paths to actual transition trajectories [1].