Journal Article

Biomolecular pleiomorphism probed by spatial interpolation of coarse models

Mirabela Rusu, Stefan Birmanns and Willy Wriggers

in Bioinformatics

Volume 24, issue 21, pages 2460-2466
Published in print November 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn461

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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.

Contact: wriggers@biomachina.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5504 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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