Molecular simulations and visualization: introduction and overview.

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

[1]  Mario Cannataro,et al.  Visualization of protein interaction networks: problems and solutions , 2013, BMC Bioinformatics.

[2]  Michael Gleicher,et al.  GRAPE: GRaphical Abstracted Protein Explorer , 2010, Nucleic Acids Res..

[3]  Mehdi Ammi,et al.  Collaborative Strategies for the Search of 3-D Targets in Molecular Environments , 2012, IEEE Transactions on Systems, Man, and Cybernetics, Part C (Applications and Reviews).

[4]  James Surowiecki The wisdom of crowds: Why the many are smarter than the few and how collective wisdom shapes business, economies, societies, and nations Doubleday Books. , 2004 .

[5]  Jean-François Méhaut,et al.  Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures. , 2009, The Journal of chemical physics.

[6]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[7]  Benjamin M. Good,et al.  Games with a scientific purpose , 2011, Genome Biology.

[8]  Shin-Yong Chen,et al.  An interactive nanomanipulation visualization based on molecular dynamics simulation and virtual reality , 2013 .

[9]  Gareth Jones,et al.  The cloud and other new computational methods to improve molecular modelling , 2014, Expert opinion on drug discovery.

[10]  Stefan Birmanns,et al.  GPU-accelerated visualization of protein dynamics in ribbon mode , 2011, Electronic Imaging.

[11]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[12]  Sidharth Thakur,et al.  Adapting Visual‐Analytical Tools for the Exploration of Structural and Dynamical Features of Polymer Conformations , 2011 .

[13]  Z. Popovic,et al.  Crystal structure of a monomeric retroviral protease solved by protein folding game players , 2011, Nature Structural &Molecular Biology.

[14]  C. Lintott,et al.  Galaxy Zoo 1: data release of morphological classifications for nearly 900 000 galaxies , 2010, 1007.3265.

[15]  Martin Falk,et al.  Atomistic Visualization of Mesoscopic Whole‐Cell Simulations Using Ray‐Casted Instancing , 2013, Comput. Graph. Forum.

[16]  Diwakar Shukla,et al.  To milliseconds and beyond: challenges in the simulation of protein folding. , 2013, Current opinion in structural biology.

[17]  Rajkumar Buyya,et al.  Article in Press Future Generation Computer Systems ( ) – Future Generation Computer Systems Cloud Computing and Emerging It Platforms: Vision, Hype, and Reality for Delivering Computing as the 5th Utility , 2022 .

[18]  Benjamin M. Good,et al.  Crowdsourcing for bioinformatics , 2013, Bioinform..

[19]  Nathan DeBardeleben,et al.  An investigation of the effects of hard and soft errors on graphics processing unit‐accelerated molecular dynamics simulations , 2014, Concurr. Comput. Pract. Exp..

[20]  Jonathan D Hirst,et al.  Molecular Dynamics Simulations Using Graphics Processing Units , 2011, Molecular informatics.

[21]  Alfredo Pulvirenti,et al.  Tools and collaborative environments for bioinformatics research , 2011, Briefings Bioinform..

[22]  J. Iwasa Animating the model figure. , 2010, Trends in cell biology.

[23]  Xin Wu,et al.  Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform. , 2012, Journal of chemical theory and computation.

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

[25]  Easwar Krishna Iyer Cloud Computing and its Leveling Impact between Developed and Emerging Economies , 2013 .

[26]  Joseph A. Bank,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .

[27]  SHUIGENG ZHOU,et al.  When Cloud Computing Meets Bioinformatics: a Review , 2013, J. Bioinform. Comput. Biol..

[28]  Simon McIntosh-Smith,et al.  Massively Multicore Parallelization of Kohn-Sham Theory. , 2008, Journal of chemical theory and computation.

[29]  Matthieu Chavent,et al.  MetaMol: high-quality visualization of molecular skin surface. , 2008, Journal of molecular graphics & modelling.

[30]  Ivan Viola,et al.  Visual cavity analysis in molecular simulations , 2013, BMC Bioinformatics.

[31]  Antoine Ferreira,et al.  Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality , 2008, Microelectron. J..

[32]  Peter M. Kasson,et al.  Computational Biology in the Cloud: Methods and New Insights from Computing at Scale , 2012, Pacific Symposium on Biocomputing.

[33]  Seok-Hee Hong,et al.  Visualization of the interactome: What are we looking at? , 2012, Proteomics.

[34]  Klaus Schulten,et al.  Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware , 2010, ISVC.

[35]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[36]  Gaël McGill,et al.  Molecular Movies… Coming to a Lecture near You , 2008, Cell.

[37]  Marc Baaden,et al.  THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES , 2014 .

[38]  Mehdi Ammi,et al.  Haptic Communication Tools for Collaborative Deformation of Molecules , 2012, EuroHaptics.

[39]  D. Goodsell,et al.  Visualization of macromolecular structures , 2010, Nature Methods.

[40]  John Bohannon Grassroots Supercomputing , 2005, Science.

[41]  Mark S Gordon,et al.  Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi. , 2014, Journal of chemical theory and computation.

[42]  Sébastien Limet,et al.  Interactive Molecular Dynamics: Scaling up to Large Systems , 2013, ICCS.

[43]  Daniel Baum,et al.  Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale , 2012, Comput. Graph. Forum.

[44]  Damien Larivière,et al.  Easy DNA Modeling and More with GraphiteLifeExplorer , 2013, PloS one.

[45]  Valerie Daggett,et al.  Analyzing Disease-Associated Protein Structures with Visual Analytics , 2013, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

[46]  Sophia Kossida,et al.  State-of-the-art technology in modern computer-aided drug design , 2013, Briefings Bioinform..

[47]  David J. Zielinski,et al.  KinImmerse: Macromolecular VR for NMR ensembles , 2008, Source Code for Biology and Medicine.

[48]  Marc Baaden,et al.  Complex molecular assemblies at hand via interactive simulations , 2009, J. Comput. Chem..

[49]  Michael Gleicher,et al.  Ieee Transactions on Visualization and Computer Graphics Automated Illustration of Molecular Flexibility , 2022 .

[50]  Moritz P. Haag,et al.  Real‐time quantum chemistry , 2012, 1208.3717.

[51]  Garrett M Morris,et al.  The emerging role of cloud computing in molecular modelling. , 2013, Journal of molecular graphics & modelling.

[52]  Matthieu Chavent,et al.  Bendix: intuitive helix geometry analysis and abstraction , 2012, Bioinform..

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

[54]  Tobias Isenberg,et al.  Illustrative Molecular Visualization with Continuous Abstraction , 2011, Comput. Graph. Forum.

[55]  Eric Lonstein,et al.  Prize-based contests can provide solutions to computational biology problems , 2013, Nature Biotechnology.

[56]  Alex Pentland,et al.  Time-Critical Social Mobilization , 2010, Science.

[57]  Ani Anciaux-Sedrakian,et al.  Accelerating VASP electronic structure calculations using graphic processing units , 2012, J. Comput. Chem..

[58]  Daniel Baum,et al.  Exploring cavity dynamics in biomolecular systems , 2013, BMC Bioinformatics.

[59]  Marc Baaden,et al.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. , 2014, Chemical Society reviews.

[60]  Toshihisa Takagi,et al.  Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era , 2012, BMC Genomics.

[61]  Mehdi Ammi,et al.  Multisensory VR interaction for protein-docking in the CoRSAIRe project , 2009, Virtual Reality.

[62]  Thomas Ertl,et al.  Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Coherent Culling and Shading for Large Molecular Dynamics Visualization , 2022 .

[63]  Z. Popovic,et al.  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players , 2012, Nature Biotechnology.

[64]  Aaron Sisto,et al.  Ab initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework. , 2014, Accounts of chemical research.

[65]  Zhihan Lv,et al.  Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges , 2013, PloS one.

[66]  Paolo Cignoni,et al.  Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization , 2006, IEEE Transactions on Visualization and Computer Graphics.

[67]  Klaus Schulten,et al.  GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.

[68]  Alexandre M J J Bonvin,et al.  Advances in integrative modeling of biomolecular complexes. , 2013, Methods.

[69]  Klaus Schulten,et al.  Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories , 2012, EuroVis.

[70]  David S. Goodsell,et al.  ePMV embeds molecular modeling into professional animation software environments. , 2011, Structure.

[71]  Alexandre Gillet,et al.  Tangible interfaces for structural molecular biology. , 2005, Structure.

[72]  Nicola Zonta,et al.  Accessible haptic technology for drug design applications , 2009, Journal of molecular modeling.

[73]  Antony J. Williams,et al.  The Spectral Game: leveraging Open Data and crowdsourcing for education , 2009, J. Cheminformatics.

[74]  W. Michael Brown,et al.  Implementing molecular dynamics on hybrid high performance computers - Three-body potentials , 2013, Comput. Phys. Commun..

[75]  Gert Vriend,et al.  YASARA View—molecular graphics for all devices—from smartphones to workstations , 2014, Bioinform..

[76]  L. Pauling,et al.  THE ARCHITECTURE OF MOLECULES. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

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

[78]  Stefan Bruckner,et al.  Style Transfer Functions for Illustrative Volume Rendering , 2007, Comput. Graph. Forum.

[79]  Stefan Birmanns,et al.  Immersive structural biology: a new approach to hybrid modeling of macromolecular assemblies , 2009, Virtual Reality.

[80]  Adrien Treuille,et al.  Predicting protein structures with a multiplayer online game , 2010, Nature.

[81]  Thomas Ertl,et al.  Interactive Visualization of Molecular Surface Dynamics , 2009, IEEE Transactions on Visualization and Computer Graphics.

[82]  Xavier Andrade,et al.  Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods. , 2013, Journal of chemical theory and computation.

[83]  Robert M Farber,et al.  Topical perspective on massive threading and parallelism. , 2011, Journal of molecular graphics & modelling.

[84]  Adam K. L. Wong,et al.  The Design and Implementation of the VMD Plugin for NAMD Simulations on the Amazon Cloud , 2012, CloudCom 2012.

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

[86]  Thomas E. Ferrin,et al.  Workshop on molecular animation. , 2010, Structure.

[87]  Ivan Viola,et al.  Implicit representation of molecular surfaces , 2012, 2012 IEEE Pacific Visualization Symposium.

[88]  Michael Gleicher,et al.  Using a commodity high-definition television for collaborative structural biology , 2014, Journal of applied crystallography.

[89]  David Baker,et al.  Algorithm discovery by protein folding game players , 2011, Proceedings of the National Academy of Sciences.

[90]  Matthieu Chavent,et al.  Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations , 2012 .

[91]  Salvatore Lanzavecchia,et al.  Image and volume data rotation with 1- and 3-pass algorithms , 1996, Comput. Appl. Biosci..

[92]  Marco Callieri,et al.  Intuitive representation of surface properties of biomolecules using BioBlender , 2012, BMC Bioinformatics.

[93]  Todd J. Martinez,et al.  Graphical Processing Units for Quantum Chemistry , 2008, Computing in Science & Engineering.

[94]  O. Delalande,et al.  Elucidation by NMR solution of neurotensin in small unilamellar vesicle environment: molecular surveys for neurotensin receptor recognition , 2013, Journal of biomolecular structure & dynamics.

[95]  Charles Marion,et al.  A hybrid visualization system for molecular models , 2013, Web3D '13.

[96]  Koji Yasuda,et al.  Accelerating Density Functional Calculations with Graphics Processing Unit. , 2008, Journal of chemical theory and computation.

[97]  Li Guo,et al.  Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics. , 2013, Journal of molecular graphics & modelling.

[98]  Joseph R Weber,et al.  ProteinShader: illustrative rendering of macromolecules , 2009, BMC Structural Biology.

[99]  Samuel Hertig,et al.  A guide to the visual analysis and communication of biomolecular structural data , 2014, Nature Reviews Molecular Cell Biology.

[100]  Andrea Brancale,et al.  Haptic-driven applications to molecular modeling: state-of-the-art and perspectives. , 2012, Future medicinal chemistry.

[101]  Torsten Schwede,et al.  Protein modeling: what happened to the "protein structure gap"? , 2013, Structure.

[102]  Cameron Mura,et al.  Ten Simple Rules for Creating Biomolecular Graphics , 2014, ArXiv.

[103]  Tobias Hoppe,et al.  Stereoscopic cell visualization: from mesoscopic to molecular scale , 2014, J. Electronic Imaging.

[104]  Bruno Lévy,et al.  GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids , 2011, J. Comput. Chem..

[105]  Thomas Ertl,et al.  GPU-powered tools boost molecular visualization , 2011, Briefings Bioinform..

[106]  Andrej Sali,et al.  Uncertainty in integrative structural modeling. , 2014, Current opinion in structural biology.

[107]  Jerome BaudryCorresponding authorUT,et al.  High-throughput virtual molecular docking with AutoDockCloud , 2012 .

[108]  Berk Hess,et al.  Algorithm improvements for molecular dynamics simulations , 2011 .

[109]  A. Olson,et al.  Student Learning about Biomolecular Self-Assembly Using Two Different External Representations , 2013, CBE life sciences education.

[110]  Thomas Ertl,et al.  Object-space ambient occlusion for molecular dynamics , 2012, 2012 IEEE Pacific Visualization Symposium.

[111]  Chris-Kriton Skylaris,et al.  Porting ONETEP to graphical processing unit‐based coprocessors. 1. FFT box operations , 2013, J. Comput. Chem..

[112]  Thierry Matthey,et al.  ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization , 2001, PPSC.

[113]  Sergey I. Bozhevolnyi,et al.  Gap , 2020, Encyclopedic Dictionary of Archaeology.