title: Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.
abstract: Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition of the structure. Theoretical approaches have become then the alternative but face serious timescale problems, since many biologically relevant deformation movements happen in a timescale that is far beyond the possibility of current atomistic models. In this complex scenario, coarse-grained simulation methods have emerged as a powerful and inexpensive alternative. Along this chapter, we will review these coarse-grained methods, and explain their physical foundations and their range of applicability.
authors.affiliation: Joint IRB-BSC Program on Computational Biology, Barcelona Supercomputing Center and Institute of Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Laura
authors.initials: L
authors.lastname: Orellana
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.forename: Athi N
authors.initials: AN
authors.lastname: Naganathan
authors.forename: Agustí
authors.initials: A
authors.lastname: Emperador
authors.forename: Oliver
authors.initials: O
authors.lastname: Carrillo
authors.forename: J L
authors.initials: JL
authors.lastname: Gelpí
mesh_terms: D030562:Databases, Protein; D006801:Humans; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins