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Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules
Author(s) -
Zhang Zhiyong,
Wriggers Willy
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20983
Subject(s) - orthogonalization , principal component analysis , eigenvalues and eigenvectors , statistical physics , feature (linguistics) , representation (politics) , basis (linear algebra) , covariance , computer science , biological system , dynamics (music) , mathematics , algorithm , physics , artificial intelligence , quantum mechanics , geometry , biology , statistics , linguistics , philosophy , politics , political science , acoustics , law
Multivariate statistical methods are widely used to extract functional collective motions from macromolecular molecular dynamics (MD) simulations. In principal component analysis (PCA), a covariance matrix of positional fluctuations is diagonalized to obtain orthogonal eigenvectors and corresponding eigenvalues. The first few eigenvectors usually correspond to collective modes that approximate the functional motions in the protein. However, PCA representations are globally coherent by definition and, for a large biomolecular system, do not converge on the time scales accessible to MD. Also, the forced orthogonalization of modes leads to complex dependencies that are not necessarily consistent with the symmetry of biological macromolecules and assemblies. Here, we describe for the first time the application of local feature analysis (LFA) to construct a topographic representation of functional dynamics in terms of local features. The LFA representations are low dimensional, and like PCA provide a reduced basis set for collective motions, but they are sparsely distributed and spatially localized. This yields a more reliable assignment of essential dynamics modes across different MD time windows. Also, the intrinsic dynamics of local domains is more extensively sampled than that of globally coherent PCA modes. Proteins 2006. © 2006 Wiley‐Liss, Inc.