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Bioinformatics Advance Access originally published online on August 30, 2008
Bioinformatics 2008 24(21):2460-2466; doi:10.1093/bioinformatics/btn461
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Biomolecular pleiomorphism probed by spatial interpolation of coarse models

Mirabela Rusu , Stefan Birmanns and Willy Wriggers *,{dagger}

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

*To whom correspondence should be addressed.


  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.

Contact: wriggers{at}biomachina.org

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}Present address: D. E. Shaw Research, 39th Floor, 120 West 45th Street, New York, NY 10036, USA.

Associate Editor: Anna Tramontano

Received on May 19, 2008; revised on July 23, 2008; accepted on August 25, 2008

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