Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
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Authors: | Márton Münz Rune Lyngsø Jotun Hein Philip C Biggin |
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Affiliation: | (1) Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK;(2) Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK;(3) Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK |
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Abstract: | Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. |
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