Bringing Molecular Dynamics Simulation Data into View

Hildebrand, Peter W.; Rose, Alexander S.; Tiemann, Johanna K. S.

doi:10.1016/j.tibs.2019.06.004

Title: Bringing Molecular Dynamics Simulation Data into View

Journal Article · 10 July 2019 · Trends in Biochemical Sciences

DOI: https://doi.org/10.1016/j.tibs.2019.06.004 · OSTI ID:1564312

Hildebrand, Peter W. ^[1]; Rose, Alexander S. ^[2]; Tiemann, Johanna K. S. ^[3]

Leipzig Univ. (Germany); Charite - Universitatsmedizin, Berlin (Germany); Berlin Inst. of Health (BIH) (Germany)
Univ. of California, San Diego, CA (United States)
Leipzig Univ. (Germany)

Molecular Dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that by providing intuitive and interactive visualization along with related protocols and analysis data promotes understanding, reliability, and re-usability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

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Research Organization:: RCSB Protein Data Bank (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG); Berlin Institute of Health (BIH); Einstein Center Digital Future; National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: SC0019749

OSTI ID:: 1564312

Alternate ID(s):: OSTI ID: 1601255

Journal Information:: Trends in Biochemical Sciences, Vol. 44, Issue 11; ISSN 0968-0004

Publisher:: Cell PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 90 works

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References (62)

Biomolecular Simulation: A Computational Microscope for Molecular Biology Dror, Ron O.; Dirks, Robert M.; Grossman, J. P. Annual Review of Biophysics, Vol. 41, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155245	journal	June 2012
Molecular dynamics simulations of large macromolecular complexes Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith Current Opinion in Structural Biology, Vol. 31 https://doi.org/10.1016/j.sbi.2015.03.007	journal	April 2015
Precision vs Flexibility in GPCR signaling Elgeti, Matthias; Rose, Alexander S.; Bartl, Franz J. Journal of the American Chemical Society, Vol. 135, Issue 33 https://doi.org/10.1021/ja405133k	journal	August 2013
The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin Manglik, Aashish; Kobilka, Brian Current Opinion in Cell Biology, Vol. 27 https://doi.org/10.1016/j.ceb.2014.01.008	journal	April 2014
Position of Transmembrane Helix 6 Determines Receptor G Protein Coupling Specificity Rose, Alexander S.; Elgeti, Matthias; Zachariae, Ulrich Journal of the American Chemical Society, Vol. 136, Issue 32 https://doi.org/10.1021/ja5055109	journal	July 2014
Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations Wingler, Laura M.; Elgeti, Matthias; Hilger, Daniel Cell, Vol. 176, Issue 3 https://doi.org/10.1016/j.cell.2018.12.005	journal	January 2019
Structural Insights into the Process of GPCR-G Protein Complex Formation Liu, Xiangyu; Xu, Xinyu; Hilger, Daniel Cell, Vol. 177, Issue 5 https://doi.org/10.1016/j.cell.2019.04.021	journal	May 2019
Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture) Levitt, Michael Angewandte Chemie International Edition, Vol. 53, Issue 38 https://doi.org/10.1002/anie.201403691	journal	August 2014
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field Lee, Jumin; Cheng, Xi; Swails, Jason M. Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00935	journal	December 2015
High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD Doerr, Stefan; Giorgino, Toni; Martínez-Rosell, Gerard Journal of Chemical Theory and Computation, Vol. 13, Issue 9 https://doi.org/10.1021/acs.jctc.7b00480	journal	August 2017
NGL Viewer: a web application for molecular visualization Rose, Alexander S.; Hildebrand, Peter W. Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv402	journal	April 2015
NGL viewer: web-based molecular graphics for large complexes Rose, Alexander S.; Bradley, Anthony R.; Valasatava, Yana Bioinformatics, Vol. 34, Issue 21 https://doi.org/10.1093/bioinformatics/bty419	journal	May 2018
Toward Theoretical Techniques for Measuring the Use of Human Effort in Visual Analytic Systems Crouser, R. Jordan; Franklin, Lyndsey; Endert, Alex IEEE Transactions on Visualization and Computer Graphics, Vol. 23, Issue 1 https://doi.org/10.1109/TVCG.2016.2598460	journal	January 2017
Familiarity Vs Trust: A Comparative Study of Domain Scientists' Trust in Visual Analytics and Conventional Analysis Methods Dasgupta, Aritra; Lee, Joon-Yong; Wilson, Ryan IEEE Transactions on Visualization and Computer Graphics, Vol. 23, Issue 1 https://doi.org/10.1109/TVCG.2016.2598544	journal	January 2017
Molecular simulations and visualization: introduction and overview Hirst, Jonathan D.; Glowacki, David R.; Baaden, Marc Faraday Discuss., Vol. 169 https://doi.org/10.1039/C4FD90024C	journal	January 2014
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Web Apps Come of Age for Molecular Sciences Abriata, Luciano Informatics, Vol. 4, Issue 3 https://doi.org/10.3390/informatics4030028	journal	August 2017
Augmenting Research, Education, and Outreach with Client-Side Web Programming Abriata, Luciano A.; Rodrigues, João P. G. L. M.; Salathé, Marcel Trends in Biotechnology, Vol. 36, Issue 5 https://doi.org/10.1016/j.tibtech.2017.11.009	journal	May 2018
Announcing the worldwide Protein Data Bank Berman, Helen; Henrick, Kim; Nakamura, Haruki Nature Structural & Molecular Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nsb1203-980	journal	December 2003
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1004	journal	October 2018
The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki Structure, Vol. 20, Issue 3 https://doi.org/10.1016/j.str.2012.01.010	journal	March 2012
State-of-the-Art Report in Web-based Visualization Mwalongo, F.; Krone, M.; Reina, G. Computer Graphics Forum, Vol. 35, Issue 3 https://doi.org/10.1111/cgf.12929	journal	June 2016
GPU-based remote visualization of dynamic molecular data on the web Mwalongo, Finian; Krone, Michael; Becher, Michael Graphical Models, Vol. 88 https://doi.org/10.1016/j.gmod.2016.05.001	journal	November 2016
MegaMol—A Prototyping Framework for Particle-Based Visualization Grottel, Sebastian; Krone, Michael; Muller, Christoph IEEE Transactions on Visualization and Computer Graphics, Vol. 21, Issue 2 https://doi.org/10.1109/TVCG.2014.2350479	journal	February 2015
MDsrv: viewing and sharing molecular dynamics simulations on the web Tiemann, Johanna K. S.; Guixà-González, Ramon; Hildebrand, Peter W. Nature Methods, Vol. 14, Issue 12 https://doi.org/10.1038/nmeth.4497	journal	December 2017
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P. Biophysical Journal, Vol. 109, Issue 8 https://doi.org/10.1016/j.bpj.2015.08.015	journal	October 2015
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B. Journal of Computational Chemistry, Vol. 32, Issue 10 https://doi.org/10.1002/jcc.21787	journal	April 2011
HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data Carrillo-Tripp, Mauricio; Alvarez-Rivera, Leonardo; Lara-Ramírez, Omar Israel Journal of Computer-Aided Molecular Design, Vol. 32, Issue 8 https://doi.org/10.1007/s10822-018-0141-y	journal	August 2018
GROMACS: A message-passing parallel molecular dynamics implementation Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Computer Physics Communications, Vol. 91, Issue 1-3 https://doi.org/10.1016/0010-4655(95)00042-E	journal	September 1995
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
Highlights of (bio-)chemical tools and visualization software for computational science Dubbeldam, David; Vreede, Jocelyne; Vlugt, Thijs JH Current Opinion in Chemical Engineering, Vol. 23 https://doi.org/10.1016/j.coche.2019.02.001	journal	March 2019
Analysis of impact metrics for the Protein Data Bank Markosian, Christopher; Di Costanzo, Luigi; Sekharan, Monica Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2018.212	journal	October 2018
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Afgan, Enis; Baker, Dannon; Batut, Bérénice Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky379	journal	May 2018
A Golden Age for Working with Public Proteomics Data Martens, Lennart; Vizcaíno, Juan Antonio Trends in Biochemical Sciences, Vol. 42, Issue 5 https://doi.org/10.1016/j.tibs.2017.01.001	journal	May 2017
A global coalition to sustain core data Anderson, Warwick P. Nature, Vol. 543, Issue 7644 https://doi.org/10.1038/543179a	journal	March 2017
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Sali, Andrej; Berman, Helen M.; Schwede, Torsten Structure, Vol. 23, Issue 7 https://doi.org/10.1016/j.str.2015.05.013	journal	July 2015
A New Generation of Crystallographic Validation Tools for the Protein Data Bank Read, Randy J.; Adams, Paul D.; Arendall, W. Bryan Structure, Vol. 19, Issue 10 https://doi.org/10.1016/j.str.2011.08.006	journal	October 2011
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data Hospital, Adam; Andrio, Pau; Cugnasco, Cesare Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1301	journal	November 2015
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings Thibault, Julien C.; Cheatham, Thomas E.; Facelli, Julio C. Journal of Chemical Information and Modeling, Vol. 54, Issue 6 https://doi.org/10.1021/ci500173w	journal	May 2014
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing Thibault, Julien C.; Roe, Daniel R.; Facelli, Julio C. Journal of Cheminformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1758-2946-6-4	journal	January 2014
An empirical analysis of journal policy effectiveness for computational reproducibility Stodden, Victoria; Seiler, Jennifer; Ma, Zhaokun Proceedings of the National Academy of Sciences, Vol. 115, Issue 11 https://doi.org/10.1073/pnas.1708290115	journal	March 2018
ActivePapers: a platform for publishing and archiving computer-aided research Hinsen, Konrad F1000Research, Vol. 3 https://doi.org/10.12688/f1000research.5773.2	journal	January 2014
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems Elofsson, Arne; Hess, Berk; Lindahl, Erik PLOS Computational Biology, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pcbi.1006649	journal	January 2019
Data Sharing Longo, Dan L.; Drazen, Jeffrey M. New England Journal of Medicine, Vol. 374, Issue 3 https://doi.org/10.1056/NEJMe1516564	journal	January 2016
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions Lotz, Samuel D.; Dickson, Alex Journal of the American Chemical Society, Vol. 140, Issue 2 https://doi.org/10.1021/jacs.7b08572	journal	January 2018
Jmol – a paradigm shift in crystallographic visualization Hanson, Robert M. Journal of Applied Crystallography, Vol. 43, Issue 5 https://doi.org/10.1107/S0021889810030256	journal	September 2010
3Dmol.js: molecular visualization with WebGL Rego, N.; Koes, D. Bioinformatics, Vol. 31, Issue 8 https://doi.org/10.1093/bioinformatics/btu829	journal	December 2014
Molmil: a molecular viewer for the PDB and beyond Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R. Journal of Cheminformatics, Vol. 8, Issue 1 https://doi.org/10.1186/s13321-016-0155-1	journal	August 2016
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data Sehnal, David; Deshpande, Mandar; Vařeková, Radka Svobodová Nature Methods, Vol. 14, Issue 12 https://doi.org/10.1038/nmeth.4499	journal	December 2017
Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design Yuan, Shuguang; Chan, H. C. Stephen; Hu, Zhenquan Trends in Biotechnology, Vol. 35, Issue 6 https://doi.org/10.1016/j.tibtech.2017.03.009	journal	June 2017
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins Mixcoha, Edgar; Rosende, Roberto; Garcia-Fandino, Rebeca Bioinformatics, Vol. 32, Issue 21 https://doi.org/10.1093/bioinformatics/btw289	journal	June 2016
Dynameomics: A Comprehensive Database of Protein Dynamics van der Kamp, Marc W.; Schaeffer, R. Dustin; Jonsson, Amanda L. Structure, Vol. 18, Issue 4 https://doi.org/10.1016/j.str.2010.01.012	journal	March 2010
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions Newport, Thomas D.; Sansom, Mark S. P.; Stansfeld, Phillip J. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1047	journal	November 2018
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories Meyer, Tim; D'Abramo, Marco; Hospital, Adam Structure, Vol. 18, Issue 11 https://doi.org/10.1016/j.str.2010.07.013	journal	November 2010
Reproducibility vs. Replicability: A Brief History of a Confused Terminology Plesser, Hans E. Frontiers in Neuroinformatics, Vol. 11 https://doi.org/10.3389/fninf.2017.00076	journal	January 2018
Web3DMol: interactive protein structure visualization based on WebGL Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx383	journal	May 2017
Membrane cholesterol access into a G-protein-coupled receptor Guixà-González, Ramon; Albasanz, José L.; Rodriguez-Espigares, Ismael Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms14505	journal	February 2017

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59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
molecular dynamics
trajectory
interactive visualization
web-based
sharing
molecular graphics

Title: Bringing Molecular Dynamics Simulation Data into View

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Cited By (5)

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