Journal
STRUCTURE
Volume 23, Issue 12, Pages 2365-2376Publisher
CELL PRESS
DOI: 10.1016/j.str.2015.10.013
Keywords
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Funding
- MRC [G0600084, MR/N009614/1]
- Leverhulme Trust [RPG-2012-519]
- BBSRC [BB/K01692X/1]
- Arnold and Mabel Beckman foundation
- PEW charitable trust
- NIH [R01GM096089]
- Biotechnology and Biological Sciences Research Council [BB/K01692X/1] Funding Source: researchfish
- Medical Research Council [MR/J000825/1, G0600084] Funding Source: researchfish
- BBSRC [BB/K01692X/1] Funding Source: UKRI
- MRC [MR/J000825/1, G0600084] Funding Source: UKRI
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We have developed a genetic algorithm for building macromolecular complexes using only a 3D-electron microscopy density map and the atomic structures of the relevant components. For efficient sampling the method uses map feature points calculated by vector quantization. The fitness function combines a mutual information score that quantifies the goodness of fit with a penalty score that helps to avoid clashes between components. Testing the method on ten assemblies (containing 3-8 protein components) and simulated density maps at 10, 15, and 20 angstrom resolution resulted in identification of the correct topology in 90%, 70%, and 60% of the cases, respectively. We further tested it on four assemblies with experimental maps at 7.2-23.5 angstrom resolution, showing the ability of the method to identify the correct topology in all cases. We have also demonstrated the importance of the map feature-point quality on assembly fitting in the lack of additional experimental information.
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