Polish Bioinformatics Society

The review covers coarse-grained protein models: their design, representation, energy functions and sampling of conformational space. The review paper focuses also on prospective applications of coarse-grained models including: protein structure prediction, modeling of dynamic processes, protein interactions and modeling of membrane proteins. Some of the most successful applications have been achieved by the combination of coarse-grained models with a wide range of computational techniques, including classical all-atom modeling and implementation of restraints derived from various sources of experimental data.

The figure below shows application ranges for molecular modeling at different resolutions: quantum, all-atom, coarse-grained, and mesoscale. The approximate ranges of time scales and system sizes (lengths) are presented. Classical molecular modeling at all-atom resolution, while very successful, is limited by timescales and the size of protein systems. Lowering the level of protein representation from all-atom to coarse-grained opens up new opportunities for modeling of proteins and their complexes.