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Bioinformatics. 2008 Nov 1;24(21):2460-6. doi: 10.1093/bioinformatics/btn461. Epub 2008 Aug 30.

Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

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  • 1School of Health Information Sciences, University of Texas Health Science Center at Houston, 7000 Fannin St, Suite 600, Houston, TX 77030, USA.

Abstract

In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the biological system by feature vectors, such methods can provide a flexible approximation of the molecular structure. We have compared three well-known interpolation techniques and evaluated the results by comparing them with constrained molecular dynamics. One method, inverse distance weighting interpolation, consistently produced models that were nearly indistinguishable on the alpha carbon level from the molecular dynamics results. The method is simple to apply and enables flexing of structures by non-expert modelers. This is useful for the basic interpretation of volumetric data in biological applications such as electron microscopy. The method can be used as a general interpretation tool for sparsely sampled motions derived from coarse models.

PMID:
18757874
[PubMed - indexed for MEDLINE]
PMCID:
PMC2732278
Free PMC Article
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