Efficient pebble game algorithms engineered for protein rigidity applications

摘要

Pebble game rigidity analysis is an efficient method for extracting rigidity and flexibility information of biomolecules without performing costly molecular dynamics simulations. The standard algorithm works on a multi-graph associated to a mechanical model constructed from an arbitrary atom-bond network. Motivated by large scale protein flexibility and simulated unfolding applications, we have developed a faster and more robust variation tailored to the specificities of bio-polymers. We describe this new phased pebble game as implemented in the new version of our software Kinari-2.