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Modelling of bacteriophage capsids and free nucleic acids
Author(s) -
Zipper Peter,
Durchschlag Helmut
Publication year - 2007
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/s0021889807005936
Subject(s) - icosahedral symmetry , nucleic acid , bacteriophage , biological system , simulated annealing , ab initio , computer science , capsid , bacteriophage ms2 , statistical physics , algorithm , chemistry , physics , crystallography , biology , biochemistry , escherichia coli , gene , organic chemistry
The reconstruction of sphere shells as realized in bacteriophage capsids can be achieved by ab initio modelling approaches based on a genetic algorithm or simulated annealing. The application of tight constraints such as icosahedral symmetry makes the DAMMIN procedure the method of choice. The ab initio models obtained may be compared with three‐dimensional models derived from crystal data. This information, in conjunction with surface calculations and application of specific hydration algorithms, allows the generation of biophysically relevant hydrated three‐dimensional models. Modelling free RNA of viruses represents another challenge to advanced modelling intentions. While application of the DAMMIN procedure provides the generation of appropriate models for the overall structure of nucleic acids, inclusion of further constraints improves the biological relevance of the resultant models. This may be achieved by our in‐house program SUBSTRUCT , which allows involvement of secondary structure details.