Characterizing the morphology of protein binding patches
DSpace at IIT Bombay
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Title |
Characterizing the morphology of protein binding patches
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Creator |
MALOD-DOGNIN, N
BANSAL, A CAZALS, F |
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Subject |
protein complex
binding patch interface morphology structural comparisons voronoi models shelling tree tree edit distance dynamic programming-based comparisons TREE EDIT DISTANCE COMPUTATIONAL DESIGN RECOGNITION SITES SCORING FUNCTIONS INTERFACES DOCKING ALGORITHM SURFACE IMMUNOGLOBULINS IDENTIFICATION |
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Description |
Let the patch of a partner in a protein complex be the collection of atoms accounting for the interaction. To improve our understanding of the structurefunction relationship, we present a patch model decoupling the topological and geometric properties. While the geometry is classically encoded by the atomic positions, the topology is recorded in a graph encoding the relative position of concentric shells partitioning the interface atoms. The topologicalgeometric duality provides the basis of a generic dynamic programming-based algorithm comparing patches at the shell level, which may favor topological or geometric features. On the biological side, we address four questions, using 249 cocrystallized heterodimers organized in biological families. First, we dissect the morphology of binding patches and show that Nature enjoyed the topological and geometric degrees of freedom independently while retaining a finite set of qualitatively distinct topological signatures. Second, we argue that our shell-based comparison is effective to perform atomic-level comparisons and show that topological similarity is a less stringent than geometric similarity. We also use the topological versus geometric duality to exhibit topo-rigid patches, whose topology (but not geometry) remains stable upon docking. Third, we use our comparison algorithms to infer specificity-related information amidst a database of complexes. Finally, we exhibit a descriptor outperforming its contenders to predict the binding affinities of the affinity benchmark. The softwares developed with this article are available from http://team.inria.fr/abs/vorpatch_compatch/.
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Publisher |
WILEY-BLACKWELL
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Date |
2014-10-15T16:56:14Z
2014-10-15T16:56:14Z 2012 |
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Type |
Article
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Identifier |
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80(12)2652-2665
http://dx.doi.org/10.1002/prot.24144 http://dspace.library.iitb.ac.in/jspui/handle/100/15265 |
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Language |
en
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