Modelling of bacteriophage capsids and free nucleic acids

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 in...

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Bibliographic Details
Published in:Journal of applied crystallography 2007-04, Vol.40 (s1), p.s153-s158
Main Authors: Zipper, Peter, Durchschlag, Helmut
Format: Article
Language:English
Subjects:
Bacteria
bacteriophages
Biochemistry
Biophysics
capsids
Crystal structure
Crystallography
modelling approaches
nucleic acids
small-angle X-ray scattering
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Summary: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.
ISSN:1600-5767
0021-8898
1600-5767
DOI:10.1107/S0021889807005936