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Fingerprint‐based structure retrieval using electron density
Author(s) -
Yin Shuangye,
Dokholyan Nikolay V.
Publication year - 2011
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.22941
Subject(s) - electron density , fingerprint (computing) , electron microscope , electron , zernike polynomials , simple (philosophy) , protein data bank , computer science , artificial intelligence , materials science , biological system , pattern recognition (psychology) , physics , molecular physics , protein structure , nuclear magnetic resonance , optics , biology , quantum mechanics , philosophy , epistemology , wavefront
We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo‐electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo‐electron microscopy. Proteins 2011. © 2010 Wiley‐Liss, Inc.