Source:http://linkedlifedata.com/resource/pubmed/id/19604479
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
7
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| pubmed:dateCreated |
2009-7-16
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| pubmed:abstractText |
In medium-resolution (7-10 A) cryo-electron microscopy (cryo-EM) density maps, alpha helices can be identified as density rods whereas beta-strand or loop regions are not as easily discerned. We are proposing a computational protein structure prediction algorithm "EM-Fold" that resolves the density rod connectivity ambiguity by placing predicted alpha helices into the density rods and adding missing backbone coordinates in loop regions. In a benchmark of 11 mainly alpha-helical proteins of known structure a native-like model is identified in eight cases (rmsd 3.9-7.9 A). The three failures can be attributed to inaccuracies in the secondary structure prediction step that precedes EM-Fold. EM-Fold has been applied to the approximately 6 A resolution cryo-EM density map of protein IIIa from human adenovirus. We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography.
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| pubmed:grant | |
| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
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| pubmed:month |
Jul
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| pubmed:issn |
1878-4186
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| pubmed:author | |
| pubmed:issnType |
Electronic
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| pubmed:day |
15
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| pubmed:volume |
17
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
990-1003
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| pubmed:meshHeading |
pubmed-meshheading:19604479-Adenoviruses, Human,
pubmed-meshheading:19604479-Algorithms,
pubmed-meshheading:19604479-Amino Acid Sequence,
pubmed-meshheading:19604479-Animals,
pubmed-meshheading:19604479-Cattle,
pubmed-meshheading:19604479-Computational Biology,
pubmed-meshheading:19604479-Computer Simulation,
pubmed-meshheading:19604479-Cryoelectron Microscopy,
pubmed-meshheading:19604479-Crystallography, X-Ray,
pubmed-meshheading:19604479-Databases, Protein,
pubmed-meshheading:19604479-Humans,
pubmed-meshheading:19604479-Microscopy, Electron,
pubmed-meshheading:19604479-Models, Chemical,
pubmed-meshheading:19604479-Models, Molecular,
pubmed-meshheading:19604479-Molecular Sequence Data,
pubmed-meshheading:19604479-Monte Carlo Method,
pubmed-meshheading:19604479-Protein Conformation,
pubmed-meshheading:19604479-Protein Folding,
pubmed-meshheading:19604479-Protein Structure, Secondary,
pubmed-meshheading:19604479-Proteins,
pubmed-meshheading:19604479-ROC Curve,
pubmed-meshheading:19604479-Rhodopsin,
pubmed-meshheading:19604479-Sequence Homology, Amino Acid,
pubmed-meshheading:19604479-Software
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| pubmed:year |
2009
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| pubmed:articleTitle |
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.
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| pubmed:affiliation |
Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA.
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| pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.,
Research Support, N.I.H., Extramural
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