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http://vision.unipv.it/ ANALYSIS OF GEMOMETRICAL AND TOPOLOGICAL ATTITUDE FOR PROTEIN-PROTEIN INTERACTION VIRGINIO CANTONI, LUCE LOMBARDI, RICCARDO GATTI Dipartimento di Informatica e Sistemistica, Universit di PAVIA, { virginio.cantoni,

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ANALYSIS OF GEMOMETRICAL AND TOPOLOGICAL ATTITUDE FOR PROTEIN-PROTEIN INTERACTION

VIRGINIO CANTONI, LUCE LOMBARDI, RICCARDO GATTI Dipartimento di Informatica e Sistemistica, Università di PAVIA, {virginio.cantoni, luca.lombardi, riccardo gatti}@unipv.it

http://vision.unipv.it/

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Overview

  • Study the interaction between structures

and other molecules (Protein Docking)

– Molecular surface representation – Protein surface analysis – Geometric shape descriptors – Shape matching algorithms

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3 September 13, 2011 PR PS BB 2011

Surface Modeling

Convex hull Van der Waals surface Solvent accessibile surface Solvent-excluded surface

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4 September 13, 2011 PR PS BB 2011

Mathermatical morphology: Closing Operation

Dilation Erosion

The structural element is a sphere representing the solvent

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Docking Protein-Protein Interfaces

The docking site is more planar rather than a cavity.

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Convex Hull

Note that straight lines (facet in 3D) are represented in a point in the EGI, and their „spike‟ can be easily eliminated, leaving only the true contour (surface) of the

  • bject (protein).

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7 September 13, 2011 PR PS BB 2011

A CH of a molecule (1MK5)

  • The CH of a molecule is

the smallest convex polyhedron that contains the molecule

  • A practical O(n log n)

algorithm for general dimensions CH computing, is Quickhull (Barber, 1996)

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Propagation in concavity volume from CH

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Propagation in the concavitiy volume

  • The concavity volume is the

region R between the CH and the SES

  • BCH is the set of the border

voxels of CH

  • A is the increasing set of voxels

contained in R; E is to the recruited near neighbors

  • dn + wn is the minimum distance

in the near neighbors by the displacement w

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10 September 13, 2011 PR PS BB 2011

A E D C B F g I h L a g b

Propagation in the CV: 2D sketch

A B C D E F I L g h

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Back-propagation for pockets and tunnels search (1MK5)

The vertical clusters not associated to any pockets are black, the ones representing pockets are colored

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Pockets detected on the 1MK5

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Protein Inspector – finding pockets

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Protein Inspector: pockets refinement

All pockets at once with TD constraint

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Protein Inspector – pockets refinement

Single pocket with TD and ligand box constraints

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The main pocket

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The second main pocket

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The main pocket of 1MK5

  • Adjacent atoms

– green from CASTp – Red and green from PPS

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1MK5

Credits: SW by Riccardo Gatti

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Protein Inspector – finding protrusions

Segmentation of protrusions for a 2D shape

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Protein Inspector – finding protrusions

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Protein inspector – user interface

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2D sketch for searching protuberances

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Active sites matching

  • Two data structures are proposed:

– the Concavity Tree

Arcelli C, Sanniti di Baja G (1978) “Polygonal covering and concavity tree of binary digital pictures”, Proceeding International Conference MECO ‟78, Athens, pp. 292–297.

– the Extended Gaussian Image

Hu, Z., · Chung, R., · Fung K. S. M., (2010), “EC-EGI: enriched complex EGI for 3D shape registration”, Machine Vision and Applications, 2, 177–188.

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Concavity Tree

A B C D A1 A2 C1 D2 D1 B1 B2 B3 B21 B22 B11 B31 B33 B32 B12 B311 B331 B321 B111 B2 B3 B1 B211 25

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Concavity Tree

A B C D

A1 A2 D1 C1 D2 B1 B2 B3 B11 B12 B22 B21 B31 B32 B33 B311 B321 B331 B111 B211

First level Second level Third level Fourth level

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Protein 1MK5

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Protein 1MK5 concavity tree

June 8, 2011 28

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Concavity tree

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30 September 13, 2011 PR PS BB 2011

CT: node content

  • Volume
  • Surface to Volume

Ratio

  • Skewness of Height

Distribution

  • Kurtosis of Height

Distribution

  • Mouth Aperture
  • Travel Depth
  • Top Five Peaks and

Valleys

  • Summit Density
  • Mean Summit

Curvatures

  • Interfacial Area Ratio
  • Residue Conservation

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Protein-protein interaction

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Protein-protein interaction

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CAPRI: Critical Assessment of PRediction of Interactions

  • CAPRI (Critical Assessment of PRedicted

Interaction) is an international effort, aimed at objectively assessing the performance of these methods by inviting developers to test their algorithms on the same protein targets and objectively evaluating the results.

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