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Molecular replacement with multiple different models
Author(s) -
Glykos Nicholas M.,
Kokkinidis Michael
Publication year - 2004
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889803027390
Subject(s) - molecular replacement , generalization , generality , computer science , algorithm , curse of dimensionality , mathematics , artificial intelligence , crystal structure , chemistry , crystallography , psychology , mathematical analysis , psychotherapist
Classical molecular replacement methods and the newer six‐dimensional searches treat molecular replacement as a succession of sub‐problems of reduced dimensionality. Due to their `divide‐and‐conquer' approach, these methods necessarily ignore (at least during their early stages) the very knowledge that a target crystal structure may comprise, for example, more than one copy of a search model, or several models of different types. An algorithm for a stochastic multi‐dimensional molecular replacement search has been described previously and shown to locate solutions successfully, even in cases as complex as a 23‐dimensional 4‐body search. The original description of the method only dealt with a special case of molecular replacement, namely with the problem of placing n copies of only one search model in the asymmetric unit of a target crystal structure. Here a natural generalization of this algorithm is presented to deal with the full molecular replacement problem, that is, with the problem of determining the orientations and positions of a total of n copies of m different models (with n ≥ m ) which are assumed to be present in the asymmetric unit of a target crystal structure. The generality of this approach is illustrated through its successful application to a 17‐dimensional 3‐model problem involving one DNA and two protein molecules.