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Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations [article]

Junghoon Chae, Debsindhu Bhowmik, Heng Ma, Arvind Ramanathan, Chad Steed
<span title="2019-11-04">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon  ...  We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations.  ...  Finally, to the best of our knowledge, this is the first interactive visualization for deep embeddings of MD simulations. III. EMBEDDING OF MOLECULAR DYNAMICS SIMULATIONS A.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/830844">doi:10.1101/830844</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fhmqbdal5jdn7btzmcb5pqeihm">fatcat:fhmqbdal5jdn7btzmcb5pqeihm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711030354/https://www.biorxiv.org/content/biorxiv/early/2019/11/04/830844.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/84/718465215e0efb8727ad84cea44ba1b79640ae86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/830844"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Physics-Based Visual Characterization of Molecular Interaction Forces

Pedro Hermosilla, Jorge Estrada, Victor Guallar, Timo Ropinski, Alvar Vinacua, Pere-Pau Vazquez
<span title="">2017</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hjrujdrg7zaghbdsp5pdzq7cmm" style="color: black;">IEEE Transactions on Visualization and Computer Graphics</a> </i> &nbsp;
Abstract-Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering.  ...  We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions  ...  We have realized this interactive visual analysis by including the following visual idioms: filtering, focus and context, feature enhancement, and interaction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2016.2598825">doi:10.1109/tvcg.2016.2598825</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27875187">pmid:27875187</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ijbgcfy7qraxxhiwuexxlvmwpa">fatcat:ijbgcfy7qraxxhiwuexxlvmwpa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724135710/https://upcommons.upc.edu/bitstream/handle/2117/98321/vis2016_largeRangeInteractionSubmittedBlack.pdf;jsessionid=59AC9CB9617B3F46045CDC6B995C59A7?sequence=6" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cb/ce/cbce57a815dd931f2530d6b3502f3424c3a70ef4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2016.2598825"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Temporal Focus+Context for Clusters in Particle Data [article]

Joachim Staib, Sebastian Grottel, Stefan Gumhold
<span title="">2017</span> <i title="The Eurographics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uejqaqophvfzfnp6en7i2lzslq" style="color: black;">International Symposium on Vision, Modeling, and Visualization</a> </i> &nbsp;
Inspired from illustrative techniques, we present an interactive focus+context visualization, based on flow ribbons, that combines both approaches.  ...  Time-dependent particle-based simulations are typically carried out by direct calculation of interactions between particles over time.  ...  Data Preprocessing Our method is laid out with a focus in molecular dynamics and thermodynamics. Data sets in these areas typically consist of particles that move and interact, but do not vanish.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/vmv.20171263">doi:10.2312/vmv.20171263</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/vmv/StaibGG17.html">dblp:conf/vmv/StaibGG17</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iiaivbfeafaxnieg4kga25rrqa">fatcat:iiaivbfeafaxnieg4kga25rrqa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220120000228/https://diglib.eg.org/xmlui/bitstream/handle/10.2312/vmv20171263/085-093.pdf;jsessionid=6F326745959C3A68FDF87C020A6CC1F7?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/14/2514eb7d6ee8dbaef40579f0dc96170a4eb5493f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/vmv.20171263"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Particle methods in natural science and engineering

Christian Holm, Thomas Ertl, Siegfried Schmauder, Johannes Kästner, Joachim Gross
<span title="">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvlzfoi7gra73gfdc2tmci5zsy" style="color: black;">The European Physical Journal Special Topics</a> </i> &nbsp;
Especially useful are particle-based molecular dynamics (MD) simulations since from an accurate description of the pair interactions of microscopic particles it is possible to deduce the macroscopic material  ...  "dynamical simulations of systems with large particle numbers".  ...  The main research focus was on the development of methods that assist the interactive and explorative visual analysis of large, dynamic molecular data sets on single desktop computers, often with GPU-accelerated  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1140/epjst/e2019-900008-2">doi:10.1140/epjst/e2019-900008-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/shgn647bd5hufpv5owgvsg76tq">fatcat:shgn647bd5hufpv5owgvsg76tq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501232345/https://link.springer.com/content/pdf/10.1140%2Fepjst%2Fe2019-900008-2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/99/56/9956f0569d0dcbc6ad28bcfac653426f1806b8ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1140/epjst/e2019-900008-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Illustrative Timelapse: A technique for illustrative visualization of particle-based simulations

Mathieu Le Muzic, Manuela Waldner, Julius Parulek, Ivan Viola
<span title="">2015</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/553mn3ftxzcw3dqndtflgqwduq" style="color: black;">2015 IEEE Pacific Visualization Symposium (PacificVis)</a> </i> &nbsp;
Our real-time technique lets us observe results of mesoscale particle simulation in fast-forward while showcasing perceivable moving molecules and a scene full of stochastic motion and interactions ABSTRACT  ...  , (2) visual abstraction of molecular trajectories to ensure that observers are able to visually follow the main actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve  ...  We would also like thank the collaborators of this project, Stefan Brckner, Helwing Hauser, Matthias Ziegler and Matthias Bernhard.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/pacificvis.2015.7156384">doi:10.1109/pacificvis.2015.7156384</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/apvis/MuzicWPV15.html">dblp:conf/apvis/MuzicWPV15</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qw4jjummrvaz7nynt7w2mqkugq">fatcat:qw4jjummrvaz7nynt7w2mqkugq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829051308/https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/lemuzic_2015_timelapse-paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/74/1e/741ef02e800a3ff6a6fae6bbfaa27ac7e6439225.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/pacificvis.2015.7156384"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Visualizing time-related data in biology, a review

Maria Secrier, Reinhard Schneider
<span title="2013-04-12">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Here, we review some advances in biological visualization of timedriven processes and consider how they aid data analysis and interpretation.  ...  This has driven related advances in visualization and analysis tools that try to effectively exploit this data.  ...  Her research focuses on developing visualization tools for the analysis of dynamic patterns and phenotypic outcomes in biological processes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbt021">doi:10.1093/bib/bbt021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23585583">pmid:23585583</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4171679/">pmcid:PMC4171679</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i4poftxlujgqfao7t7kw22zhqi">fatcat:i4poftxlujgqfao7t7kw22zhqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729151347/https://watermark.silverchair.com/bbt021.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAZswggGXBgkqhkiG9w0BBwagggGIMIIBhAIBADCCAX0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM4EWBi5CKIZl9dYF1AgEQgIIBTp8HttioOMi7GImdOeq-GXwCFTEOB58LOthgZoMGomDJnzUUKQhJkboCfahx0ARoz4ZyWww3im-fm5IVyuwOf8WfPcGw3E2o9vtbrNy9OpvEAQHS25YzC4OCa3rTWtz0KGhKubD-g2rf3ANkp0mM4PnSbWE3myxFofybTBv6LFCSBSaklKPmZVe5YkG-GIRdXkkP7sr1cHWUtkFKC3bFzRkiqu9A1xui3u3amjLgVsxioetw7qAK_wU-jpOGDaig56eF3Fnehe6IElqddPN-JsmoU2lWptSqZ4R3lRTN9Fk6bHfOaXxijTT9ieBle_QpsR9NHczdLwHrfQvIjJldEJxY_iMge4NeXh3WQhQEMBWN5oLmt9ko4cMNLfRfiy7wDtdb6qGWQC0k0vHrkeIKbwrkX7JGDty1dN43I_V4CHxo-qt8zwl90-LSyPeBo68" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/68/f168febcc5cd8d83f46208deb07d3a829b545749.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbt021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171679" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From Virtual Reality to Immersive Analytics in Bioinformatics

Björn Sommer, Marc Baaden, Michael Krone, Andrew Woods
<span title="2018-06-26">2018</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
Often, the visualization and exploration of related structural – usually molecular – data plays an important role in the aforementioned contexts.  ...  Often, these approaches provide "just" visual support of the analysis, e.g. in the case of exploring and interacting with a protein on a 3D monitor and compatible interaction hardware.  ...  The visualization of molecular dynamics has a long tradition, using standard tools such as VMD or PyMol.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2018-0043">doi:10.1515/jib-2018-0043</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29982237">pmid:29982237</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a5qan3jpg5bvvije733fg24yqq">fatcat:a5qan3jpg5bvvije733fg24yqq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428124605/https://kops.uni-konstanz.de/bitstream/handle/123456789/44587/Sommer_2-r9qr3r0k0eg95.pdf;jsessionid=19AAA078875EC532CD5F3E4826ED6CA6?sequence=3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c2/30/c23090034ba36702a439addf086c4dc45ed1323e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2018-0043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

Molecular Visualization of Computational Biology Data: A Survey of Surveys [article]

Naif Alharbi, Mohammad Alharbi, Xavier Martinez, Michael Krone, Alexander S. Rose, Marc Baaden, Robert S. Laramee, Matthieu Chavent
<span title="">2017</span> <i title="The Eurographics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvnub6swsjfnhdwblr4kp44pry" style="color: black;">Eurographics Conference on Visualization</a> </i> &nbsp;
It offers a distinctive step forward in managing the literature on visualization of molecular dynamics and related simulation approaches.  ...  We apply a variety of data-driven analysis to highlight links or differences between studies from both communities.  ...  Acknowledgments We would like to thank the Ministry of Education of Saudi Arabia and the Saudi Cultural Bureau in London for financial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/eurovisshort.20171146">doi:10.2312/eurovisshort.20171146</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/vissym/AlharbiAMKRBLC17.html">dblp:conf/vissym/AlharbiAMKRBLC17</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/efbnkc6ftfepzhn6b63mozqmuy">fatcat:efbnkc6ftfepzhn6b63mozqmuy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220114134527/https://diglib.eg.org/xmlui/bitstream/handle/10.2312/eurovisshort20171146/133-137.pdf;jsessionid=2287612AC8EA6D676128E27F051A3CDF?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/16/1a/161af626f19c920437615791b91e30c626ac8f12.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/eurovisshort.20171146"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Visual cavity analysis in molecular simulations

Julius Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Additionally, we interactively visualize the graphs in the context of the molecular surface.  ...  Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule.  ...  We would also like to thank Helwig Hauser and Visualization group in Bergen for useful ideas and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s19-s4">doi:10.1186/1471-2105-14-s19-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564409">pmid:24564409</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3980935/">pmcid:PMC3980935</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2km2nh7vzvd2njdsiumgewmklu">fatcat:2km2nh7vzvd2njdsiumgewmklu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720020917/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S19-S4?site=bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/e4/bce441c12c45235b264b66d57e8468c07e4d255c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s19-s4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980935" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Available Instruments for Analyzing Molecular Dynamics Trajectories

I. V. Likhachev, N. K. Balabaev, O. V. Galzitskaya
<span title="2016-03-14">2016</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/thqexu3tybc35jjo7vrk2crxwi" style="color: black;">Open Biochemistry Journal</a> </i> &nbsp;
Molecular dynamics trajectories are the result of molecular dynamics simulations.  ...  The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. © Likhachev et al.; Licensee Bentham Open.  ...  This work was funded in part by the Russian Science Foundation (grant number 14-14-0536) for OVG, the programs "Molecular and Cellular Biology" (01201353567) for IVL, and grant MES RK Grant 2835/GF3 of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1874091x01610010001">doi:10.2174/1874091x01610010001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27053964">pmid:27053964</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4797681/">pmcid:PMC4797681</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qogx6q4upjdqrgfd4nvq7vssim">fatcat:qogx6q4upjdqrgfd4nvq7vssim</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723111223/https://benthamopen.com/contents/pdf/TOBIOCJ/TOBIOCJ-10-1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e4/20/e420c2ce582d77f11dabde5a7fc4e75bb9bd66a4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1874091x01610010001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797681" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Techniques for the Visualization of Topological Defect Behavior in Nematic Liquid Crystals

Vadim Slavin, Robert Pelcovits, George Loriot, Andrew Callan-Jones, David Laidlaw
<span title="">2006</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hjrujdrg7zaghbdsp5pdzq7cmm" style="color: black;">IEEE Transactions on Visualization and Computer Graphics</a> </i> &nbsp;
time steps; it extends the use of tools developed for visualizing diffusion tensor data, re-interpreting them in the context of molecular simulations; and it has answered long-standing questions regarding  ...  We present visualization tools for analyzing molecular simulations of liquid crystal (LC) behavior.  ...  Physicists use simulation techniques-including molecular dynamics and Monte Carlo algorithms-that are based on a theoretical understanding of the complex molecular interactions between LC molecules [2  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2006.182">doi:10.1109/tvcg.2006.182</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17080868">pmid:17080868</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5vybjonasvbx5cya2qmdecu4ja">fatcat:5vybjonasvbx5cya2qmdecu4ja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923005425/http://cs.brown.edu/research/pubs/pdfs/2006/Slavin-2006-TVT.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8c/b6/8cb686180599a052c634d52b7a99161353915464.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2006.182"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

VIA-MD: Visual Interactive Analysis of Molecular Dynamics [article]

Robin Skånberg, Mathieu Linares, Carolin König, Patrick Norman, Daniel Jönsson, Ingrid Hotz, Anders Ynnerman
<span title="">2018</span> <i title="The Eurographics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5wphw5mzfnbzhmmvfxizgjuggq" style="color: black;">Workshop on Molecular Graphics and Visual Analysis of Molecular Data</a> </i> &nbsp;
The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations  ...  We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data.  ...  The prototype of this project has been implemented using the visualization framework Inviwo [Inv] and immediate mode GUI Dear ImGui [Cor].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/molva.20181102">doi:10.2312/molva.20181102</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/molva-ws/SkanbergLKNJHY18.html">dblp:conf/molva-ws/SkanbergLKNJHY18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cwtzkbsrovdk3gut3k6c352ndi">fatcat:cwtzkbsrovdk3gut3k6c352ndi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220113080007/https://diglib.eg.org/xmlui/bitstream/handle/10.2312/molva20181102/019-027.pdf;jsessionid=293D098D7C39FB2861A4439321451CFF?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/ba/a0bae46333616246c284c16bc31c744ef5289eac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2312/molva.20181102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose
<span title="2021-05-06">2021</span> <i title="Oxford University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level  ...  The performance requirements for visualization and analysis tools delivering these data are increasing rapidly.  ...  , and specifically Dr Shuchismita Dutta for providing the basis of the User documentation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab314">doi:10.1093/nar/gkab314</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33956157">pmid:33956157</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8262734/">pmcid:PMC8262734</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zwxfdrql6fdarhjcmw7wv4rvaq">fatcat:zwxfdrql6fdarhjcmw7wv4rvaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210803215353/https://watermark.silverchair.com/gkab314.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsIwggK-BgkqhkiG9w0BBwagggKvMIICqwIBADCCAqQGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMCvcnNYvyxyeUqXQOAgEQgIICdVCdEi6H5Cy70fszMZVoayNIM4oiHsmSWAbcDeD8qSvKIZzCx2jUjOjNnCYSIPRFwN1JlKaAYN5VfOr7c5H5lhQEDtpUDr6GG88ihqYrtmSCWinCwpNN4Hzc527NmNyZK00hQ2tWCKLiVxF3bZ32j1W0oV-ThbwLJBxHsdKiUokn3q1810St9e7VtkdiS3Q_mDQotmin3zu5Ue4XLI8QVp-yWLjcheoFGpfvDX2_gCce9xceoNlEtiMN5c57sA1EzP1bqJ0_Z4bOazKgs-lGFInD1BDcmVN-3kqfOVmUsMOsA-gkc-uZK_x2sVrBOXpq7uXRTjmK5vHZNGCWu5pCeY1SKty9NeH__iuwgkaaKmveQrtXprdh_xy7S6rArggJxsrk0uM8qqVlwygs2Hwx286AAz1Hl9XOrFA6ZoRbR_IGzaHD18fArh67EaZqTXHpk-59AwJCTljKnY4wF5ujAznMP-0NlptMtneDi-Njc6cYVzZngNxPS8i_XccSsNYZlfQHuZ-pNTlHjCB12p5h99gBSziPMVs9uOIsdgy6fVozqf2DUI3Q2rFU5og2deLCHkl1D2TEQ08DMN9gW0AlSMkuerlLjVed0s9g-D_63Dcszj8RXnKx9jSJB09imQpHPAM5EoTrh5cOUrJg5ThYipGsLzXHoCAIU_misp_npmb-4UWOQiqF5SbryjjkQv9aE2lx7AsRwWvrsIIdvkpUlIBRGvZe0rSpoFog0KQUXYBVXzkeazQneKGqgoOb-gRBD57XucUfugKnU8uQltwd9PhT396PRfQpmk-NrXxhhDO5whFJei0XHyvWwUeSjSdR1Tqd89hN" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0c/0c/0c0ce9cebd2ad2b9607b52e2bd4db9ddb58686b1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab314"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262734" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations

Hrachya Astsatryan, Wahi Narsisian, Eliza Gyulgyulyan, Vardan Baghdasaryan, Armen Poghosyan, Yevgeni Mamasakhlisov, Peter Wittenburg
<span title="2018-05-10">2018</span> <i title="Scalable Computing: Practice and Experience"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7l2kwu7zkvgr7hdwfzmx2x6mcm" style="color: black;">Scalable Computing : Practice and Experience</a> </i> &nbsp;
The article aims to introduce an integrated web-based interactive data platform for molecular dynamic simulations using the datasets generated by different life science communities from Armenia.  ...  We focus on interactive data visualization workflow service as a key to perform more in-depth analyzes of research data outputs, helping to understand the problems efficiently and to consolidate the data  ...  the Republic of Armenia.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12694/scpe.v19i2.1337">doi:10.12694/scpe.v19i2.1337</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vuuyee52wngvroxftclunjkq2a">fatcat:vuuyee52wngvroxftclunjkq2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428153923/https://www.scpe.org/index.php/scpe/article/download/1337/536" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/52/29/52294404ca059fce387c76f7e5197d5cc9f75775.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12694/scpe.v19i2.1337"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions

Robin Skanberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz
<span title="2021-01-14">2021</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hjrujdrg7zaghbdsp5pdzq7cmm" style="color: black;">IEEE Transactions on Visualization and Computer Graphics</a> </i> &nbsp;
This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles.  ...  In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time.  ...  Molecular Visualization and Analysis -Numerous software packages have been developed and are widely used to visualize molecular dynamics trajectories.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2021.3051632">doi:10.1109/tvcg.2021.3051632</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33444141">pmid:33444141</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w26oyymzyben3iehccqihruyii">fatcat:w26oyymzyben3iehccqihruyii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210801185856/http://liu.diva-portal.org/smash/get/diva2:1538629/FULLTEXT01" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1e/2c/1e2ca99944e3e1600dcd701f271f0b8e20919ca3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tvcg.2021.3051632"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>
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