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Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Abstract:

In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging from helical pores such as gramicidin and small beta-barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the C(alpha)-atom traject...

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Publication status:
Published

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Publisher copy:
10.1002/prot.20257

Authors


Faraldo-Gómez, JD More by this author
Forrest, LR More by this author
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Journal:
Proteins
Volume:
57
Issue:
4
Pages:
783-791
Publication date:
2004-12-05
DOI:
EISSN:
1097-0134
ISSN:
0887-3585
URN:
uuid:35860ca1-f57d-4bd5-9b06-a8e402963818
Source identifiers:
100459
Local pid:
pubs:100459

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