VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr OUTLINE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 2/23 INTRODUCTION • Protein structure • Motivation for protein analysis • Channel detection VISUALIZATION OF PROTEIN STRUCTURES • Visualization techniques• Visualization techniques • State of the art visualization software CURRENT RESULTS • CAVER Viewer Software • Future work CONCLUSION HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr PROTEIN STRUCTURE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 3/23 • Thousands to tens of thousands of atoms • Groups of atoms forming residues, which are connected together with peptide bond • All residues form a polypeptidic chain = single protein molecule HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr MOTIVATION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 4/23 • Analysis leading to channel computation • All chemical reactions between protein and substrate take place in the active site • Checking the possibility of entering substrate into protein molecule • Channels are substantial for creating new compounds, especially in drug design HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 5/23 • Protein molecule HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 6/23 • Active site HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 7/23 • Small molecule of substrate HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 8/23 • Approximation of the substrate molecule ( bounding box) HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 9/23 • Computed channel HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 10/23 • Another posible channel HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 11/23 • Second channel is too narrow HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CHANNEL DETECTION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 12/23 • The best possible channel HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr VISUALIZATION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 13/23 Sticks Alpha Trace HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr Lines Sticks Alpha Trace Balls and sticks Balls (VDW Radii) Secondary Structures CHANNEL VISUALIZATION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 14/23 HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr Balls Tetrahedrons -> Surface subdivision Points VISUALIZATION APPLICATIONS VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 15/23 • Many applications developed • Only few widely used (PyMOL, VMD…) HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 16/23 • Software combining protein analysis and visualisation, developed in cooperation with biochemists from the Loschmidt Laboratories, Faculty of Science, MU • 3000 users of caver viewer od pymol plugin around the world of both academic and commercial sphere • Advanced features for further channel exploration HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr • Advanced features for further channel exploration CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 17/23 HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 18/23 • Properties of channels (lenghts, widths, curvature…) • 2D and 3D graphs HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 19/23 • Graph statistics HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 20/23 • Depth visualization • Creating selections HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr CAVER VIEWER SOFTWARE VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 21/23 • Clipping plane HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr FUTURE WORK VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 22/23 • Analysis and visualisation of large proteins and other biochemical strucures (e.g. Ribosoms (~ 100 000 atoms) • Visualisation of large dynamic molecular trajectories (~ 100 000 snapshots) • 100 000 atoms in 100 000 frames means ~ 120 GB of data (3 floating point HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr • 100 000 atoms in 100 000 frames means ~ 120 GB of data (3 floating point coordinates for each atom and frame) • Design and implementation of extremly effective data structures for such bulky structures enabling real-time visualisation of dynamics • Development of new visualisation techniques CONCLUSION VISUALIZATION (AND ANALYSIS) OF LARGESCALE DYNAMIC BIOCHEMICAL STRUCTURES 23/23 • Thank you! • Questions? HCI Laboratory | Faculty of Informatics | Masaryk University Vilém Šustr XYZ VÝZKUM V OBLASTI POČÍTAČEM SIMULOVANÉ KALIGRAFIE 1/15 • abc • def Masarykova univerzita | Fakulta informatiky Vilém Šustr | Diplomová práce | Jaro 2009