Open AccessNCS‐constrained exhaustive search using oligomeric models
Author(s) -
Isupov Michail N.,
Lebedev Andrey A.
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444907053802
Subject(s) - oligomer , translation (biology) , rotation (mathematics) , function (biology) , orientation (vector space) , symmetry (geometry) , translational symmetry , value (mathematics) , algorithm , biological system , series (stratigraphy) , computer science , mathematics , statistical physics , physics , artificial intelligence , statistics , chemistry , geometry , nuclear magnetic resonance , biology , paleontology , biochemistry , evolutionary biology , messenger rna , gene
The efficiency of the cross‐rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self‐rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross‐rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.