Interactive Molecular Visualisation at the Interface

Physical and computer models of molecules are designed to embody chemical knowledge of the molecular world. Over the past forty years interactive molecular visualization software has transformed the way chemical scientists build and use molecular models. This chapter surveys interactive molecular visualization from the point of view of the molecular model, showing the convergence of its visual, haptic, and tangible instantiations, and their use to represent chemical structure and dynamics.

[1]  K. Schulten,et al.  Single-Molecule Experiments in Vitro and in Silico , 2007, Science.

[2]  D C Richardson,et al.  The kinemage: A tool for scientific communication , 1992, Protein science : a publication of the Protein Society.

[3]  Kenneth M Merz,et al.  Haptic applications for molecular structure manipulation. , 2007, Journal of molecular graphics & modelling.

[4]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[5]  K Y Sanbonmatsu,et al.  Large-scale simulations of the ribosome: a new landmark in computational biology , 2006 .

[6]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[7]  F. Crick,et al.  Molecular structure of nucleic acids , 2004, JAMA.

[8]  G Johnson,et al.  A prototype molecular interactive collaborative environment (MICE). , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[9]  A Anderson,et al.  VRDD: applying virtual reality visualization to protein docking and design. , 1999, Journal of molecular graphics & modelling.

[10]  Priya Vashishta,et al.  Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics. , 2006, The journal of physical chemistry. B.

[11]  Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation , 2003, cond-mat/0306461.

[12]  David S. Goodsell,et al.  Augmented reality with tangible auto-fabricated models for molecular biology applications , 2004, IEEE Visualization 2004.

[13]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[14]  M F Sanner,et al.  Python: a programming language for software integration and development. , 1999, Journal of molecular graphics & modelling.

[15]  John E. Johnson,et al.  The use of solid physical models for the study of macromolecular assembly. , 1998, Current opinion in structural biology.

[16]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[17]  Francis T. Marchese A stereographic table for biomolecular visualization , 2002, Proceedings Sixth International Conference on Information Visualisation.

[18]  Francis T. Marchese,et al.  Fostering Asynchronous Collaborative Visualization , 2007, 2007 11th International Conference Information Visualization (IV '07).

[19]  John Kenneth Salisbury,et al.  Haptic Rendering: Introductory Concepts , 2004, IEEE Computer Graphics and Applications.

[20]  Roald Hoffmann,et al.  Representation in Chemistry , 1989 .

[21]  Frits H. Post,et al.  Virtual Spring Manipulators for Particle Steering in Molecular Dynamics on the ResponsiveWorkbench , 2002, International Conference on Artificial Reality and Telexistence and Eurographics Symposium on Virtual Environments.

[22]  Angel Herráez,et al.  Biomolecules in the computer: Jmol to the rescue , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[23]  F. Jensen Introduction to Computational Chemistry , 1998 .

[24]  K. Schulten,et al.  Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. , 2003, Biophysical journal.

[25]  Hiroshi Ishii,et al.  Emerging frameworks for tangible user interfaces , 2000, IBM Syst. J..

[26]  Nick Hopwood,et al.  Models: The Third Dimension of Science , 2004 .

[27]  David M. Frohlich,et al.  The history and future of direct manipulation , 1993, Behav. Inf. Technol..

[28]  Eric Francoeur,et al.  From model kits to interactive computer graphics , 2004 .

[29]  Yi Pan,et al.  Adapting single-user visualization software for collaborative use , 2003, Proceedings on Seventh International Conference on Information Visualization, 2003. IV 2003..

[30]  Ying Zhu,et al.  A collaborative multi-view virtual environment for molecular visualization and modeling , 2005, Coordinated and Multiple Views in Exploratory Visualization (CMV'05).

[31]  Peter S. Lomdahl,et al.  MOLECULAR DYNAMICS COMES OF AGE: 320 BILLION ATOM SIMULATION ON BlueGene/L , 2006 .

[32]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[33]  D. C. Rapaport,et al.  Multibillion-atom molecular dynamics simulation: Design considerations for vector-parallel processing , 2006, Comput. Phys. Commun..

[34]  Yuan-Shin Lee,et al.  Interactive Computer-Aided Design for Molecular Docking and Assembly , 2006 .

[35]  L. Pauling The Nature Of The Chemical Bond , 1939 .

[36]  Thomas Ertl,et al.  Time-Based Haptic Analysis of Protein Dynamics , 2007, Second Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (WHC'07).

[37]  C. Levinthal Molecular model-building by computer. , 1966, Scientific American.

[38]  Alan Hinchliffe,et al.  Molecular Modelling for Beginners , 2003 .

[39]  Jürgen Pleiss,et al.  Integrating molecular modeling tools and virtual reality engines: an architecture for a highly immersive molecular modeling (HIMM) environment , 1998, Proceedings. Computer Graphics International (Cat. No.98EX149).

[40]  Jan F. Prins,et al.  SMD: visual steering of molecular dynamics for protein design , 1996 .

[41]  Nancy M. Amato,et al.  Ligand binding with OBPRM and user input , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).

[42]  Frederick P. Brooks,et al.  Project GROPEHaptic displays for scientific visualization , 1990, SIGGRAPH.

[43]  Lydia E. Kavraki,et al.  Molecular docking: a problem with thousands of degrees of freedom , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).

[44]  Klaus Schulten,et al.  A system for interactive molecular dynamics simulation , 2001, I3D '01.

[45]  E. Hückel,et al.  The nature of the chemical bond and the structure of molecules and crystals. — An Introduction to modern structural chemistry. von Linus Pauling. 429 S.mit 72 Fig. Ithaka, New‐York. Cornell University Press. Preis geb. 4,50 Dollar , 1940, Zeitschrift für Elektrochemie und angewandte physikalische Chemie.

[46]  Bernd Fröhlich,et al.  The Responsive Workbench [virtual work environment] , 1994, IEEE Computer Graphics and Applications.

[47]  Michael L. Raymer,et al.  PocketMol: a molecular visualization tool for the Pocket PC , 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

[48]  D. Levine,et al.  Stalk: an interactive system for virtual molecular docking , 1997 .

[49]  Jörg Meyer,et al.  Interactive 3D protein structure visualization using virtual reality , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

[50]  Benedict Leimkuhler,et al.  Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.

[51]  Robert Drees Virtual Reality in Chemistry , 1997 .

[52]  Eric Francoeur,et al.  The Forgotten Tool: The Design and Use of Molecular Models , 1997 .

[53]  Klaus Schulten,et al.  Steered Molecular Dynamics , 1999, Computational Molecular Dynamics.

[54]  Vladimir Pavlovic,et al.  Speech/gesture interface to a visual computing environment for molecular biologists , 1996, Proceedings of 13th International Conference on Pattern Recognition.

[55]  Makoto Sato,et al.  An interactive molecular visualization system for education in immersive multi-projection virtual environment , 2004, Third International Conference on Image and Graphics (ICIG'04).

[56]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.