Format

Send to

Choose Destination
Bioinformatics. 2012 Aug 1;28(15):1972-9. doi: 10.1093/bioinformatics/bts243. Epub 2012 Apr 27.

Optimal simultaneous superpositioning of multiple structures with missing data.

Author information

1
Department of Biochemistry, Brandeis University, MS009, Waltham, MA 02454, USA. dtheobald@brandeis.edu

Abstract

MOTIVATION:

Superpositioning is an essential technique in structural biology that facilitates the comparison and analysis of conformational differences among topologically similar structures. Performing a superposition requires a one-to-one correspondence, or alignment, of the point sets in the different structures. However, in practice, some points are usually 'missing' from several structures, for example, when the alignment contains gaps. Current superposition methods deal with missing data simply by superpositioning a subset of points that are shared among all the structures. This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether.

RESULTS:

Here, we present a general solution for determining an optimal superposition when some of the data are missing. We use the expectation-maximization algorithm, a classic statistical technique for dealing with incomplete data, to find both maximum-likelihood solutions and the optimal least-squares solution as a special case.

AVAILABILITY AND IMPLEMENTATION:

The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d.org.

CONTACT:

dtheobald@brandeis.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22543369
PMCID:
PMC3400950
DOI:
10.1093/bioinformatics/bts243
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center