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Segmentation of SES for Protein Structure Analysis. Virginio Cantoni, Riccardo Gatti, Luca Lombardi University of Pavia, dept. of Computer Engineering and Systems Science,Via Ferrata 1, Pavia, Italy {virginio.cantoni, riccardo.gatti, luca.lombardi}@unipv.it. Topic List.
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Segmentation of SES for Protein Structure Analysis Virginio Cantoni, Riccardo Gatti, Luca Lombardi University of Pavia, dept. of Computer Engineering and Systems Science,Via Ferrata 1, Pavia, Italy {virginio.cantoni, riccardo.gatti, luca.lombardi}@unipv.it
Topic List • Introduction to the project • Generation of surfaces and volumes • Segmentation Algorithms • Presentation of results Segmentation of SES for Protein Structure Analysis – Valencia 2010
Project background Thispaperis part of a widerresearchprogramthatstarted last year at Computer Vision Lab (http://vision.unipv.it) in Universityof Pavia. The task istouse and adaptwellknown pattern recognition, imageanalysis, 3D graphicalgorithmsto generate new and fast bioinformaticstoolsforgeometric and morfologicalanalysisofcomplex 3D structure. In particolar we are nowfocusing on: Docking Comparison Visualization … PRIN06 - Ambienti intelligenti
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • These are the commonssurfacethat are consideredduringgeometrical and topologicalproteinanalysis: Segmentation of SES for Protein Structure Analysis – Valencia 2010
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • In the discrete space the protein and the CH are defined in a cubic grid V of dimension L x M x N.The voxel resolution adopted is 0.25 Å. Segmentation of SES for Protein Structure Analysis – Valencia 2010
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • For a bettervisualization a trianglesurfaceisgeneratedwith a modifiedversion od the marchingcubesalgorithm + some relaxationstep. Segmentation of SES for Protein Structure Analysis – Valencia 2010
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • The SASisgeneratedby a Dilationoperationfrom the MathematicalMorphology. The radiusof the structureelementis 1.4 Å. Segmentation of SES for Protein Structure Analysis – Valencia 2010
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • The SESisgeneratedbyanErosionoperationfrom the MathematicalMorphologystartingfrom the SAS. The radiusof the structureelementis 1.4 Å. Segmentation of SES for Protein Structure Analysis – Valencia 2010
Van der Waals surface Convex hull Solvent-excluded surface Solvent accessibile surface Generation of the surfaces • The Quickhull algorithm, is applied to the SES. Segmentation of SES for Protein Structure Analysis – Valencia 2010
Propagation step (DT) Let us call R the region between the CH and the SES (the concavity volume) that is: 2D Example Segmentation of SES for Protein Structure Analysis – Valencia 2010
Propagation step (DT) A propagationalgorithm (DT) inside the concavity volume isperformedstartingfrom the convexhullsurface. Note thatunreachableareassuchasαβ and γ are excluded. 2D Example A a C E D b g L I F h B g Segmentation of SES for Protein Structure Analysis – Valencia 2010
Propagation step (DT) At the end a set ofconnectedcomponentisfound. We can join togetherareasthathave some voxels in common. 2D Example Segmentation of SES for Protein Structure Analysis – Valencia 2010
Propagation step (DT) We can represent the previousresultwith a tree: 2D Example A a C E D b L I g h g L I F h B F E D C B g A Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: Byapplying the previousstepsto a test protein (1MK5) we can represent the resultwith a tree : Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: An algorithmof back propagationisappliedonto the treetofindinnerregionsof interest liketunnels and pockets. Simpleconstraintrules are appliedto guide the back propagation: the minimum passage section 1 the maximum mouth aperture 2 Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: Thisis the resultwith1 = 200 and 2 = 7500; Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: Thisis the resultwith1 = 200 and 2 = 2000; Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: First pocket (startingfrom the deepest) Segmentation of SES for Protein Structure Analysis – Valencia 2010
Practical case: Second pocket Segmentation of SES for Protein Structure Analysis – Valencia 2010
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