title: FlexE: Using elastic network models to compare models of protein structure.
abstract: It is often valuable to compare protein structures to determine how similar they are. Structure comparison methods such as RMSD and GDT-TS are based solely on fixed geometry and do not take into account the intrinsic flexibility or energy landscape of the protein. We propose a method, which we call FlexE, that is based on a simple elastic network model and uses the deformation energy as measure of the similarity between two structures. FlexE can distinguish biologically relevant conformational changes from random changes, while existing geometry-based methods cannot. Additionally, FlexE incorporates the concept of thermal energy, which provides a rational way to determine when two models are "the same". FlexE provides a unique measure of the similarity between protein structures that is complementary to existing methods.
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252.
authors.forename: Alberto
authors.initials: A
authors.lastname: Perez
authors.affiliation: Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213.
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252.
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
authors.affiliation: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252.
authors.forename: Justin L
authors.initials: JL
authors.lastname: MacCallum