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Distance Geometry Methods for Protein Structure Determination

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Distance Geometry

Abstract

We review some recent advances for solving the distance geometry (DG) problems for protein structure determination. We focus on the development of a geometric buildup approach to the problems with sparse but exact distances and on the formulation of a generalized DG problem for the determination of structural ensembles with inexact distances or distance bounds. We describe the novel ideas of these approaches, show their potentials for the solution of large-scale problems in practice, and discuss their possible future developments. For some historical background, we also provide a brief introduction to the classical matrix decomposition method, the embedding algorithm, and the global smoothing algorithm for the solution of the DG problems with exact and inexact distances. Many other methods have been developed. We will not cover them all, but refer the readers to a list of papers, hoping to provide the readers with a relatively complete knowledge of the field.

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Authors and Affiliations

  1. Department of Mathematics, Iowa State University, Ames, IA, 50011, USA

    Zachary Voller & Zhijun Wu

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  1. Zachary Voller
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  2. Zhijun Wu
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Correspondence to Zhijun Wu .

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Editors and Affiliations

  1. IRISA, University of Rennes 1, avenue du General Leclerc, Rennes, 35042, France

    Antonio Mucherino

  2. , Dept of Applied Maths (IMECC-UNICAMP), State University of Campinas, Campinas, 13081, Brazil

    Carlile Lavor

  3. , LIX, Ecole Polytechnique, Palaiseau, 91128, France

    Leo Liberti

  4. Instituto Alberto Luiz Coimbra de, Pos-Graduacao e Pesquisa de, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil

    Nelson Maculan

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Voller, Z., Wu, Z. (2013). Distance Geometry Methods for Protein Structure Determination. In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds) Distance Geometry. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5128-0_8

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