Coarse Grained Modeling and Approaches to Protein Folding

摘要

The theoretical prediction of protein structures has become a field of increasing importance in both biology and physics. Reliable prediction methods in fact, would spare time consuming experimental X-ray and NMR techniques and they would represent a challenge for computational protein modeling as well. The well known limitations of all-atom models call for the development of coarse-grained protein descriptions including a minimal number of protein-like features, while being capable of mimicking the essence of protein folding mechanisms. In this paper we review the most important classes of coarse-grained protein models in order of increasing complexity, starting from (over simplified) binary models, to models with one or two reaction centers per residue. We discuss how, despite their simplification, coarse-grained models constitute a viable approach to structure prediction and they shed light on many aspects of protein-folding problem.