Background: Techniques for inferring the functions of the protein by comparing their shapeÂ similarity have been receiving a lot of attention. Proteins are functional units and their shapeÂ flexibility occupies an essential role in various biological processes. Several shape descriptors haveÂ demonstrated the capability of protein shape comparison by treating them as rigid bodies. But thisÂ may give rise to an incorrect comparison of flexible protein shapes.
Results: We introduce an efficient approach for comparing flexible protein shapes by adapting aÂ local diameter (LD) descriptor. The LD descriptor, developed recently to handle skeleton basedÂ shape deformations , is adapted in this work to capture the invariant properties of shapeÂ deformations caused by the motion of the protein backbone. Every sampled point on the proteinÂ surface is assigned a value measuring the diameter of the 3D shape in the neighborhood of thatÂ point. The LD descriptor is built in the form of a one dimensional histogram from the distributionÂ of the diameter values. The histogram based shape representation reduces the shape comparisonÂ problem of the flexible protein to a simple distance calculation between 1D feature vectors.Â Experimental results indicate how the LD descriptor accurately treats the protein shapeÂ deformation. In addition, we use the LD descriptor for protein shape retrieval and compare it toÂ the effectiveness of conventional shape descriptors. A sensitivity-specificity plot shows that the LDÂ descriptor performs much better than the conventional shape descriptors in terms of consistencyÂ over a family of proteins and discernibility across families of different proteins.
Conclusion: Our study provides an effective technique for comparing the shape of flexibleÂ proteins. The experimental results demonstrate the insensitivity of the LD descriptor to proteinÂ shape deformation. The proposed method will be potentially useful for molecule retrieval withÂ similar shapes and rapid structure retrieval for proteins. The demos and supplemental materials areÂ available on https://engineering.purdue.edu/PRECISE/LDD.
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