Molecular Surface Maps

We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surface Map concisely shows arbitrary attributes of the original molecular surface, such as biochemical properties or geometrical features. This results in an intuitive overview, which allows researchers to assess all molecular surface attributes at a glance. Our representation can be used as a visual summarization of a molecule's interface with its environment. In particular, Molecular Surface Maps simplify the analysis and comparison of different data sets or points in time. Furthermore, the map representation can be used in a Space-time Cube to analyze time-dependent data from molecular simulations without the need for animation. We show the feasibility of Molecular Surface Maps for different typical analysis tasks of biomolecular data.

[1]  Daniel Baum,et al.  Accelerated Visualization of Dynamic Molecular Surfaces , 2010, Comput. Graph. Forum.

[2]  Thomas Ertl,et al.  Interactive Extraction and Tracking of Biomolecular Surface Features , 2013, Comput. Graph. Forum.

[3]  Patrice Koehl,et al.  How round is a protein? Exploring protein structures for globularity using conformal mapping , 2014, Front. Mol. Biosci..

[4]  Junaed Sattar Snakes , Shapes and Gradient Vector Flow , 2022 .

[5]  Daniel Baum,et al.  A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules , 2006, CompLife.

[6]  A. Klibanov,et al.  The effect of water on enzyme action in organic media. , 1988, The Journal of biological chemistry.

[7]  Daisuke Kihara,et al.  3D-SURFER: software for high-throughput protein surface comparison and analysis , 2009, Bioinform..

[8]  Hugues Hoppe,et al.  Spherical parametrization and remeshing , 2003, ACM Trans. Graph..

[9]  Valerio Pascucci,et al.  Genus Oblivious Cross Parameterization: Robust Topological Management of Inter-Surface Maps , 2007, 15th Pacific Conference on Computer Graphics and Applications (PG'07).

[10]  Roman G. Efremov,et al.  PREDDIMER: a web server for prediction of transmembrane helical dimers , 2014, Bioinform..

[11]  Rüdiger Westermann,et al.  Acceleration techniques for GPU-based volume rendering , 2003, IEEE Visualization, 2003. VIS 2003..

[12]  David A. Cosgrove,et al.  A novel method of aligning molecules by local surface shape similarity , 2000, J. Comput. Aided Mol. Des..

[13]  John P. Snyder,et al.  An Album of Map Projections , 1989 .

[14]  Ming-Yong Pang,et al.  Survey on Planar Parameterization of Triangular Meshes , 2010, 2010 International Conference on Measuring Technology and Mechatronics Automation.

[15]  S. Yau,et al.  Global conformal surface parameterization , 2003 .

[16]  Thomas Ertl,et al.  Comparative Visualization of Molecular Surfaces Using Deformable Models , 2014, Comput. Graph. Forum.

[17]  R. Verger,et al.  Lipases: Interfacial Enzymes with Attractive Applications. , 1998, Angewandte Chemie.

[18]  Demetri Terzopoulos,et al.  Constraints on Deformable Models: Recovering 3D Shape and Nonrigid Motion , 1988, Artif. Intell..

[19]  M. Nardini,et al.  α/β Hydrolase fold enzymes : the family keeps growing , 1999 .

[20]  P. Groenen,et al.  Modern Multidimensional Scaling: Theory and Applications , 1999 .

[21]  G. Schneider,et al.  PocketPicker: analysis of ligand binding-sites with shape descriptors , 2007, Chemistry Central Journal.

[22]  Sergey Zhukov,et al.  An Ambient Light Illumination Model , 1998, Rendering Techniques.

[23]  Jürgen Pleiss,et al.  Identification of imine reductase‐specific sequence motifs , 2016, Proteins.

[24]  Sahand Jamal Rahi,et al.  Mapping Complicated Surfaces onto a Sphere , 2007, Int. J. Comput. Geom. Appl..

[25]  Donald H. House,et al.  Line Drawing as a Dynamic Process , 2007 .

[26]  W. Zimmermann,et al.  Optimization of carbohydrate fatty acid ester synthesis in organic media by a lipase from Candida antarctica. , 2001, Biotechnology and bioengineering.

[27]  Ole Kirk,et al.  One Biocatalyst–Many Applications: The Use of Candida Antarctica B-Lipase in Organic Synthesis , 1998 .

[28]  Rahul Singh,et al.  Global-to-local representation and visualization of molecular surfaces using deformable models , 2009, SAC '09.

[29]  S T Roweis,et al.  Nonlinear dimensionality reduction by locally linear embedding. , 2000, Science.

[30]  M. Sheelagh T. Carpendale,et al.  A Review of Temporal Data Visualizations Based on Space-Time Cube Operations , 2014, EuroVis.

[31]  B. Marx The Visual Display of Quantitative Information , 1985 .

[32]  Christian Hofbauer,et al.  SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison , 2004, J. Chem. Inf. Model..

[33]  Tamal K. Dey,et al.  An efficient computation of handle and tunnel loops via Reeb graphs , 2013, ACM Trans. Graph..

[34]  Johann Gasteiger,et al.  The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid-binding globulin activity of steroids , 1996, J. Comput. Aided Mol. Des..

[35]  Anne Verroust-Blondet,et al.  Interactive texture mapping , 1993, SIGGRAPH.

[36]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[37]  Arie E. Kaufman,et al.  Planar Visualization of Treelike Structures , 2016, IEEE Transactions on Visualization and Computer Graphics.

[38]  Yi Zheng,et al.  Structural characterization of a β-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity. , 2014, Biochimie.

[39]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[40]  Herbert Edelsbrunner,et al.  Deformable Smooth Surface Design , 1999, Discret. Comput. Geom..

[41]  James F. Blinn,et al.  A Generalization of Algebraic Surface Drawing , 1982, TOGS.

[42]  Vladislav Kraevoy,et al.  Cross-parameterization and compatible remeshing of 3D models , 2004, SIGGRAPH 2004.

[43]  Christos Faloutsos,et al.  FastMap: a fast algorithm for indexing, data-mining and visualization of traditional and multimedia datasets , 1995, SIGMOD '95.

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[45]  Hugues Hoppe,et al.  Inter-surface mapping , 2004, ACM Trans. Graph..

[46]  Thomas Ertl,et al.  Parallel Contour-Buildup algorithm for the molecular surface , 2011, 2011 IEEE Symposium on Biological Data Visualization (BioVis)..

[47]  Amy Henderson Squilacote The Paraview Guide , 2008 .

[48]  Thomas Ertl,et al.  Visual Analysis of Dynamic Protein Cavities and Binding Sites , 2014, 2014 IEEE Pacific Visualization Symposium.

[49]  J. V. Wijk Unfolding the Earth: Myriahedral Projections , 2008 .

[50]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[51]  Alla Sheffer,et al.  Practical spherical embedding of manifold triangle meshes , 2005, International Conference on Shape Modeling and Applications 2005 (SMI' 05).

[52]  Junzhou Huang,et al.  A 3D Laplacian-driven parametric deformable model , 2011, 2011 International Conference on Computer Vision.

[53]  Kimito Funatsu,et al.  New description of protein-ligand interactions using a spherical self-organizing map. , 2012, Bioorganic & medicinal chemistry.

[54]  Jürgen Pleiss,et al.  Molecular mechanism of deactivation of C. antarctica lipase B by methanol. , 2013, Journal of biotechnology.

[55]  Nikos Paragios,et al.  Deformable Medical Image Registration: A Survey , 2013, IEEE Transactions on Medical Imaging.

[56]  Torsten Hägerstraand WHAT ABOUT PEOPLE IN REGIONAL SCIENCE , 1970 .

[57]  Ivan Viola,et al.  Visualization of Biomolecular Structures: State of the Art , 2015, EuroVis.

[58]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[59]  Jürgen Pleiss,et al.  Enzyme Toolbox: Novel Enantiocomplementary Imine Reductases , 2014, Chembiochem : a European journal of chemical biology.

[60]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[61]  Daniel Weiskopf,et al.  Space-Time Visual Analytics of Eye-Tracking Data for Dynamic Stimuli , 2013, IEEE Transactions on Visualization and Computer Graphics.