title: Extracting representative structures from protein conformational ensembles.
abstract: A large number of methods generate conformational ensembles of biomolecules. Often one structure is selected to be representative of the whole ensemble, usually by clustering and selecting the structure closest to the center of the most populated cluster. We find that this structure is not necessarily the best representation of the cluster and present here two computationally inexpensive averaging protocols that can systematically provide better representations of the system, which can be more directly compared with structures from X-ray crystallography. In practice, systematic errors in the generated conformational ensembles appear to limit the maximum improvement of averaging methods.
authors: Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.
authors: Alberto
authors: A
authors: Perez
authors: Arijit
authors: A
authors: Roy
authors: Koushik
authors: K
authors: Kasavajhala
authors: Amy
authors: A
authors: Wagaman
authors: Ken A
authors: KA
authors: Dill
authors: Justin L
authors: JL
authors: MacCallum
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D004735:Energy Transfer; D019277:Entropy; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D017711:Nonlinear Dynamics; D016011:Normal Distribution; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins
keywords: CASP; averaging; clustering; ensembles; molecular dynamics; protein; root mean square deviation