Extracting representative structures from protein conformational ensembles
Alberto Perez
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Search for more papers by this authorArijit Roy
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Search for more papers by this authorKoushik Kasavajhala
Department of Chemistry, Stony Brook University, Stony Brook, New York
Search for more papers by this authorAmy Wagaman
Department of Mathematics and Statistics, Amherst College, Massachusetts
Search for more papers by this authorKen A. Dill
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Department of Chemistry, Stony Brook University, Stony Brook, New York
Department of Physics, Stony Brook University, Stony Brook, New York
Search for more papers by this authorCorresponding Author
Justin L. MacCallum
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Department of Chemistry, University of Calgary, Alberta, Canada
Correspondence to: Justin L. MacCallum, Department of Chemistry, University of Calgary, Alberta, Canada. E-mail: [email protected]Search for more papers by this authorAlberto Perez
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Search for more papers by this authorArijit Roy
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Search for more papers by this authorKoushik Kasavajhala
Department of Chemistry, Stony Brook University, Stony Brook, New York
Search for more papers by this authorAmy Wagaman
Department of Mathematics and Statistics, Amherst College, Massachusetts
Search for more papers by this authorKen A. Dill
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Department of Chemistry, Stony Brook University, Stony Brook, New York
Department of Physics, Stony Brook University, Stony Brook, New York
Search for more papers by this authorCorresponding Author
Justin L. MacCallum
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
Department of Chemistry, University of Calgary, Alberta, Canada
Correspondence to: Justin L. MacCallum, Department of Chemistry, University of Calgary, Alberta, Canada. E-mail: [email protected]Search for more papers by this authorABSTRACT
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. Proteins 2014; 82:2671–2680. © 2014 Wiley Periodicals, Inc.
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