A survey of coarse-grained methods for modeling protein conformational transitions

The decryption of transient structural changes during protein conformational transitions is essential to a detailed understanding of protein functions. To this end, coarse-grained protein structural models have proven valuable by enabling cost-effective simulation/analysis of protein conformational transitions which are too slow for all-atom molecular dynamics simulation. Here we survey state-of-the-art coarse-grained methods for protein conformational transition modeling developed in the past decade, with focus on those available online to public. We highlight the similarities and differences between these methods, and illustrate their usage in case of the T-to-R″ transition of chaperonin GroEL. This survey aims to provide researchers with a useful guide to the available tools for modeling protein conformational transitions.