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J Struct Biol. 2013 Oct;184(1):75-82. doi: 10.1016/j.jsb.2013.05.020. Epub 2013 Jun 13.

Probabilistic determination of probe locations from distance data.

Author information

1
Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, United States.

Abstract

Distance constraints, in principle, can be employed to determine information about the location of probes within a three-dimensional volume. Traditional methods for locating probes from distance constraints involve optimization of scoring functions that measure how well the probe location fits the distance data, exploring only a small subset of the scoring function landscape in the process. These methods are not guaranteed to find the global optimum and provide no means to relate the identified optimum to all other optima in scoring space. Here, we introduce a method for the location of probes from distance information that is based on probability calculus. This method allows exploration of the entire scoring space by directly combining probability functions representing the distance data and information about attachment sites. The approach is guaranteed to identify the global optimum and enables the derivation of confidence intervals for the probe location as well as statistical quantification of ambiguities. We apply the method to determine the location of a fluorescence probe using distances derived by FRET and show that the resulting location matches that independently derived by electron microscopy.

KEYWORDS:

Distance data; Electron microscopy; FRET; Probability function

PMID:
23770585
PMCID:
PMC3796062
DOI:
10.1016/j.jsb.2013.05.020
[Indexed for MEDLINE]
Free PMC Article

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