Plateforme de visualisation

Visualisation

La plateforme de visualisation offre aux chercheurs un mur de grands écrans stéréoscopiques (4,4 m de largeur et 1,8 m de hauteur) à haute résolution (résolution de 7680 x 3240) pour explorer/manipuler leurs données, visualiser des images à haute résolution (SEM, Confocal, etc.), visualiser des structures de macromolécules et des trajectoires de simulation en 3D et visualiser différentes données simultanément grâce à la grande zone de visualisation.

Contact

Responsable scientifique 

Marc Baaden
DR- UPR 9080
baaden@smplinux.de

Ingénieur plateforme 

Hubert Santuz
IE CNRS – UPR9080
hubert.santuz@ibpc.fr

Equipements

La plateforme a été utilisée pour la construction et la validation de structures résolues par cristallographie ou Cryo-EM, ou pour l’exploration de données atomiques et structurales. L’aspect immersif de la plateforme permet également d’explorer des ensembles moléculaires complexes en groupes afin de faciliter la formulation d’hypothèses. Dans la même salle, des casques de réalité virtuelle immersifs sont également disponibles, pour des ensembles de données tridimensionnelles très complexes. Des logiciels personnalisés sont développés pour exécuter des tâches hautement spécialisées, en plus d’une large gamme de logiciels communs mis à disposition pour couvrir les besoins des utilisateurs. L’équipement de la plateforme et sa convivialité la rendent idéale pour être utilisée dans un contexte plus large que la biologie ou la bioinformatique. Elle est régulièrement utilisée dans des projets d’histoire des sciences, ainsi que dans l’éducation et la vulgarisation scientifique.

Prestations

La plateforme propose aux chercheurs un mur d’écrans stéréoscopique de grande taille et de haute
résolution pour l’exploration/manipulation de leur données. Il est possible, notamment :

  •  Afficher des images hautes résolutions (MEB, Confocal, etc)
  •  Afficher des structures de macromolécules et des trajectoires de simulations en 3D (Pymol, Chimera, Coot, VMD, UnityMol, etc)
  • Visualiser simultanément différentes données grâce à la grande surface de visualisation.
  • Afficher simultanément le contenu de PC Portables (jusqu’à 4) sur le mur afin de faciliter les échanges lors de réunions.

Remerciements & Tarification

Phrase à inclure pour toute publication utilisant des résultats acquis grâce à la plateforme Mur de visualisation de l’IBPC :

The authors acknowledge access to the visualization platform of the IBPC institute that is supported by the CNRS, the « Initiative d’Excellence » program from the French State (Grant « DYNAMO », ANR-11-LABX-0011 and grant « CACSICE », ANR-11-EQPX-0008) and the Conseil Régional d’Île-de-France (SESAME grant).

——————–

La décision relative aux tarifs de la plateforme Mur de visualisation de l’IBPC (DEC247239DR02) a établi les différents tarifs suivants :

prix de vente unitaire : demi-journée (HT)

  • Clients Privés : 499.46 €
  • Clients externes académiques : 288.71 €
  • Clients partenaires : 269.82 €   — Projets financés EUROPE Coûts éligibles 263.18 € —  Projets financés ANR Coûts éligibles 200.13 €
  • Facturation interne : 269.82 €   — Projets financés EUROPE Coûts éligibles 263.18 € —  Projets financés ANR Coûts éligibles 200.13 €

Label

La plateforme est labellisé IBiSA depuis janvier 2025.

Actualités de la plateforme

Liste de publications

5511665 82TPS5CH Visu_plateforme 1 apa 50 date desc year 2076 http://www.ibpcwp.ibpc.fr/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%22A3QM6SRM%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Laurent%20et%20al.%22%2C%22parsedDate%22%3A%222025%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BLaurent%2C%20B.%2C%20Lanrezac%2C%20A.%2C%20Santuz%2C%20H.%2C%20Ferey%2C%20N.%2C%20Delalande%2C%20O.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282025%29.%20%26lt%3Bspan%20style%3D%26quot%3Bfont-variant%3Asmall-caps%3B%26quot%3B%26gt%3BBioSpring%26lt%3B%5C%2Fspan%26gt%3B%26%23x202F%3B%3A%20An%20elastic%20network%20framework%20for%20interactive%20exploration%20of%20macromolecular%20mechanics.%20%26lt%3Bi%26gt%3BProtein%20Science%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B34%26lt%3B%5C%2Fi%26gt%3B%285%29%2C%20e70130.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1002%5C%2Fpro.70130%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1002%5C%2Fpro.70130%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22%3Cspan%20style%3D%5C%22font-variant%3Asmall-caps%3B%5C%22%3EBioSpring%3C%5C%2Fspan%3E%20%3A%20An%20elastic%20network%20framework%20for%20interactive%20exploration%20of%20macromolecular%20mechanics%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benoist%22%2C%22lastName%22%3A%22Laurent%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Lanrezac%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hubert%22%2C%22lastName%22%3A%22Santuz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22Ferey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olivier%22%2C%22lastName%22%3A%22Delalande%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20BioSpring%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20is%20an%20innovative%20tool%20for%20interactive%20molecular%20modeling%20and%20simulation%2C%20designed%20to%20explore%20the%20dynamics%20of%20biological%20structures%20in%20real%20time.%20Using%20an%20augmented%20elastic%20network%20model%2C%20the%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20BioSpring%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20framework%20enables%20researchers%20to%20intuitively%20examine%20complex%20biomolecules%2C%20and%20it%20combines%20real%5Cu2010time%20feedback%20with%20the%20user%26%23039%3Bs%20experience.%20This%20capability%20makes%20it%20ideal%20for%20initial%20analysis%20of%20molecular%20systems%2C%20protein%5Cu2013protein%20and%20protein%5Cu2013%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20DNA%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20docking%2C%20protein%20mechanics%2C%20and%20protein%5Cu2013membrane%20interactions.%20The%20multi%5Cu2010resolution%20modeling%20approach%20combines%20accuracy%20and%20efficiency%2C%20supporting%20user%5Cu2010driven%20analysis%20of%20molecular%20interactions%2C%20conformational%20flexibility%2C%20and%20structural%20mechanics.%20This%20framework%20improves%20upon%20traditional%20methods%20in%20terms%20of%20robustness%2C%20accessibility%2C%20and%20ease%20of%20use%2C%20while%20requiring%20only%20modest%20computational%20resources%20and%20enabling%20a%20fast%20turnaround%20time%20to%20obtain%20initial%20results.%20It%20provides%20insights%20into%20molecular%20function%20and%20dynamics%20that%20advance%20the%20field%20of%20structural%20biology.%20Source%20code%2C%20executables%2C%20and%20examples%20for%20the%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20BioSpring%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20simulation%20engine%20are%20available%20at%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20https%3A%5C%2F%5C%2Fbiospring.mol3d.tech%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20.%22%2C%22date%22%3A%2205%5C%2F2025%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1002%5C%2Fpro.70130%22%2C%22ISSN%22%3A%220961-8368%2C%201469-896X%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fonlinelibrary.wiley.com%5C%2Fdoi%5C%2F10.1002%5C%2Fpro.70130%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222025-07-23T15%3A26%3A13Z%22%7D%7D%2C%7B%22key%22%3A%22WHUPNU2Y%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Versini%20et%20al.%22%2C%22parsedDate%22%3A%222024-01-08%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BVersini%2C%20R.%2C%20Sritharan%2C%20S.%2C%20Aykac%20Fas%2C%20B.%2C%20Tubiana%2C%20T.%2C%20Aimeur%2C%20S.%20Z.%2C%20Henri%2C%20J.%2C%20Erard%2C%20M.%2C%20N%26%23xFC%3Bsse%2C%20O.%2C%20Andreani%2C%20J.%2C%20Baaden%2C%20M.%2C%20Fuchs%2C%20P.%2C%20Galochkina%2C%20T.%2C%20Chatzigoulas%2C%20A.%2C%20Cournia%2C%20Z.%2C%20Santuz%2C%20H.%2C%20Sacquin-Mora%2C%20S.%2C%20%26amp%3B%20Taly%2C%20A.%20%282024%29.%20A%20Perspective%20on%20the%20Prospective%20Use%20of%20AI%20in%20Protein%20Structure%20Prediction.%20%26lt%3Bi%26gt%3BJournal%20of%20Chemical%20Information%20and%20Modeling%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B64%26lt%3B%5C%2Fi%26gt%3B%281%29%2C%2026%26%23x2013%3B41.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Facs.jcim.3c01361%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Facs.jcim.3c01361%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20Perspective%20on%20the%20Prospective%20Use%20of%20AI%20in%20Protein%20Structure%20Prediction%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Raphaelle%22%2C%22lastName%22%3A%22Versini%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sujith%22%2C%22lastName%22%3A%22Sritharan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Burcu%22%2C%22lastName%22%3A%22Aykac%20Fas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Thibault%22%2C%22lastName%22%3A%22Tubiana%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sana%20Zineb%22%2C%22lastName%22%3A%22Aimeur%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julien%22%2C%22lastName%22%3A%22Henri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marie%22%2C%22lastName%22%3A%22Erard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Oliver%22%2C%22lastName%22%3A%22N%5Cu00fcsse%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jessica%22%2C%22lastName%22%3A%22Andreani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Patrick%22%2C%22lastName%22%3A%22Fuchs%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tatiana%22%2C%22lastName%22%3A%22Galochkina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexios%22%2C%22lastName%22%3A%22Chatzigoulas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zoe%22%2C%22lastName%22%3A%22Cournia%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hubert%22%2C%22lastName%22%3A%22Santuz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Sacquin-Mora%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Antoine%22%2C%22lastName%22%3A%22Taly%22%7D%5D%2C%22abstractNote%22%3A%22AlphaFold2%20%28AF2%29%20and%20RoseTTaFold%20%28RF%29%20have%20revolutionized%20structural%20biology%2C%20serving%20as%20highly%20reliable%20and%20effective%20methods%20for%20predicting%20protein%20structures.%20This%20article%20explores%20their%20impact%20and%20limitations%2C%20focusing%20on%20their%20integration%20into%20experimental%20pipelines%20and%20their%20application%20in%20diverse%20protein%20classes%2C%20including%20membrane%20proteins%2C%20intrinsically%20disordered%20proteins%20%28IDPs%29%2C%20and%20oligomers.%20In%20experimental%20pipelines%2C%20AF2%20models%20help%20X-ray%20crystallography%20in%20resolving%20the%20phase%20problem%2C%20while%20complementarity%20with%20mass%20spectrometry%20and%20NMR%20data%20enhances%20structure%20determination%20and%20protein%20flexibility%20prediction.%20Predicting%20the%20structure%20of%20membrane%20proteins%20remains%20challenging%20for%20both%20AF2%20and%20RF%20due%20to%20difficulties%20in%20capturing%20conformational%20ensembles%20and%20interactions%20with%20the%20membrane.%20Improvements%20in%20incorporating%20membrane-specific%20features%20and%20predicting%20the%20structural%20effect%20of%20mutations%20are%20crucial.%20For%20intrinsically%20disordered%20proteins%2C%20AF2%5Cu2019s%20confidence%20score%20%28pLDDT%29%20serves%20as%20a%20competitive%20disorder%20predictor%2C%20but%20integrative%20approaches%20including%20molecular%20dynamics%20%28MD%29%20simulations%20or%20hydrophobic%20cluster%20analyses%20are%20advocated%20for%20accurate%20dynamics%20representation.%20AF2%20and%20RF%20show%20promising%20results%20for%20oligomeric%20models%2C%20outperforming%20traditional%20docking%20methods%2C%20with%20AlphaFold-Multimer%20showing%20improved%20performance.%20However%2C%20some%20caveats%20remain%20in%20particular%20for%20membrane%20proteins.%20Real-life%20examples%20demonstrate%20AF2%5Cu2019s%20predictive%20capabilities%20in%20unknown%20protein%20structures%2C%20but%20models%20should%20be%20evaluated%20for%20their%20agreement%20with%20experimental%20data.%20Furthermore%2C%20AF2%20models%20can%20be%20used%20complementarily%20with%20MD%20simulations.%20In%20this%20Perspective%2C%20we%20propose%20a%20%5Cu201cwish%20list%5Cu201d%20for%20improving%20deep-learning-based%20protein%20folding%20prediction%20models%2C%20including%20using%20experimental%20data%20as%20constraints%20and%20modifying%20models%20with%20binding%20partners%20or%20post-translational%20modifications.%20Additionally%2C%20a%20meta-tool%20for%20ranking%20and%20suggesting%20composite%20models%20is%20suggested%2C%20driving%20future%20advancements%20in%20this%20rapidly%20evolving%20field.%22%2C%22date%22%3A%222024-01-08%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1021%5C%2Facs.jcim.3c01361%22%2C%22ISSN%22%3A%221549-9596%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Facs.jcim.3c01361%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A00%3A32Z%22%7D%7D%2C%7B%22key%22%3A%22CSSDI3GP%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Darbar%20et%20al.%22%2C%22parsedDate%22%3A%222024%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BDarbar%2C%20R.%2C%20Santuz%2C%20H.%2C%20Taly%2C%20A.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282024%29.%20GazeMolVR%3A%20Sharing%20Eye-Gaze%20Cues%20in%20a%20Collaborative%20VR%20Environment%20for%20Molecular%20Visualization.%20%26lt%3Bi%26gt%3BProceedings%20of%20the%20International%20Conference%20on%20Mobile%20and%20Ubiquitous%20Multimedia%26lt%3B%5C%2Fi%26gt%3B%2C%207%26%23x2013%3B23.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1145%5C%2F3701571.3701599%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1145%5C%2F3701571.3701599%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22conferencePaper%22%2C%22title%22%3A%22GazeMolVR%3A%20Sharing%20Eye-Gaze%20Cues%20in%20a%20Collaborative%20VR%20Environment%20for%20Molecular%20Visualization%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rajkumar%22%2C%22lastName%22%3A%22Darbar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hubert%22%2C%22lastName%22%3A%22Santuz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Antoine%22%2C%22lastName%22%3A%22Taly%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%2212%5C%2F2024%22%2C%22proceedingsTitle%22%3A%22Proceedings%20of%20the%20International%20Conference%20on%20Mobile%20and%20Ubiquitous%20Multimedia%22%2C%22conferenceName%22%3A%22MUM%20%2724%3A%20International%20Conference%20on%20Mobile%20and%20Ubiquitous%20Multimedia%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1145%5C%2F3701571.3701599%22%2C%22ISBN%22%3A%22979-8-4007-1283-8%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fdl.acm.org%5C%2Fdoi%5C%2F10.1145%5C%2F3701571.3701599%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222025-07-23T15%3A26%3A07Z%22%7D%7D%2C%7B%22key%22%3A%22J5QNU7UD%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Ku%5Cu0165%5Cu00e1k%20et%20al.%22%2C%22parsedDate%22%3A%222023-09%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BKu%26%23x165%3B%26%23xE1%3Bk%2C%20D.%2C%20V%26%23xE1%3Bzquez%2C%20P.%2C%20Isenberg%2C%20T.%2C%20Krone%2C%20M.%2C%20Baaden%2C%20M.%2C%20By%26%23x161%3Bka%2C%20J.%2C%20Kozl%26%23xED%3Bkov%26%23xE1%3B%2C%20B.%2C%20%26amp%3B%20Miao%2C%20H.%20%282023%29.%20State%20of%20the%20Art%20of%20Molecular%20Visualization%20in%20Immersive%20Virtual%20Environments.%20%26lt%3Bi%26gt%3BComputer%20Graphics%20Forum%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Finria.hal.science%5C%2Fhal-04006531%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Finria.hal.science%5C%2Fhal-04006531%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22State%20of%20the%20Art%20of%20Molecular%20Visualization%20in%20Immersive%20Virtual%20Environments%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Ku%5Cu0165%5Cu00e1k%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pere-pau%22%2C%22lastName%22%3A%22V%5Cu00e1zquez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tobias%22%2C%22lastName%22%3A%22Isenberg%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michael%22%2C%22lastName%22%3A%22Krone%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jan%22%2C%22lastName%22%3A%22By%5Cu0161ka%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Barbora%22%2C%22lastName%22%3A%22Kozl%5Cu00edkov%5Cu00e1%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Haichao%22%2C%22lastName%22%3A%22Miao%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222023-09%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Finria.hal.science%5C%2Fhal-04006531%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A07%3A56Z%22%7D%7D%2C%7B%22key%22%3A%22A784JAKC%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Gagelin%20et%20al.%22%2C%22parsedDate%22%3A%222023-05-05%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BGagelin%2C%20A.%2C%20Largeau%2C%20C.%2C%20Masscheleyn%2C%20S.%2C%20Piel%2C%20M.%20S.%2C%20Calder%26%23xF3%3Bn-Mora%2C%20D.%2C%20Bouillaud%2C%20F.%2C%20H%26%23xE9%3Bnin%2C%20J.%2C%20%26amp%3B%20Miroux%2C%20B.%20%282023%29.%20Molecular%20determinants%20of%20inhibition%20of%20UCP1-mediated%20respiratory%20uncoupling.%20%26lt%3Bi%26gt%3BNature%20Communications%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B14%26lt%3B%5C%2Fi%26gt%3B%281%29%2C%202594.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-023-38219-9%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-023-38219-9%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Molecular%20determinants%20of%20inhibition%20of%20UCP1-mediated%20respiratory%20uncoupling%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Antoine%22%2C%22lastName%22%3A%22Gagelin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Corentin%22%2C%22lastName%22%3A%22Largeau%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sandrine%22%2C%22lastName%22%3A%22Masscheleyn%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mathilde%20S.%22%2C%22lastName%22%3A%22Piel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%22%2C%22lastName%22%3A%22Calder%5Cu00f3n-Mora%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fr%5Cu00e9d%5Cu00e9ric%22%2C%22lastName%22%3A%22Bouillaud%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J%5Cu00e9r%5Cu00f4me%22%2C%22lastName%22%3A%22H%5Cu00e9nin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Miroux%22%7D%5D%2C%22abstractNote%22%3A%22Brown%20adipose%20tissue%20expresses%20uncoupling%20protein%201%20%28UCP1%29%2C%20which%20dissipates%20energy%20as%20heat%2C%20making%20it%20a%20target%20for%20treating%20metabolic%20disorders.%20Here%2C%20we%20investigate%20how%20purine%20nucleotides%20inhibit%20respiration%20uncoupling%20by%20UCP1.%20Our%20molecular%20simulations%20predict%20that%20GDP%20and%20GTP%20bind%20UCP1%20in%20the%20common%20substrate%20binding%20site%20in%20an%20upright%20orientation%2C%20where%20the%20base%20moiety%20interacts%20with%20conserved%20residues%20R92%20and%20E191.%20We%20identify%20a%20triplet%20of%20uncharged%20residues%2C%20F88%5C%2FI187%5C%2FW281%2C%20forming%20hydrophobic%20contacts%20with%20nucleotides.%20In%20yeast%20spheroplast%20respiration%20assays%2C%20both%20I187A%20and%20W281A%20mutants%20increase%20the%20fatty%20acid-induced%20uncoupling%20activity%20of%20UCP1%20and%20partially%20suppress%20the%20inhibition%20of%20UCP1%20activity%20by%20nucleotides.%20The%20F88A%5C%2FI187A%5C%2FW281A%20triple%20mutant%20is%20overactivated%20by%20fatty%20acids%20even%20at%20high%20concentrations%20of%20purine%20nucleotides.%20In%20simulations%2C%20E191%20and%20W281%20interact%20with%20purine%20but%20not%20pyrimidine%20bases.%20These%20results%20provide%20a%20molecular%20understanding%20of%20the%20selective%20inhibition%20of%20UCP1%20by%20purine%20nucleotides.%22%2C%22date%22%3A%222023-05-05%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41467-023-38219-9%22%2C%22ISSN%22%3A%222041-1723%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.nature.com%5C%2Farticles%5C%2Fs41467-023-38219-9%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T07%3A44%3A39Z%22%7D%7D%2C%7B%22key%22%3A%22DJ8FEJVB%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Corey%20et%20al.%22%2C%22parsedDate%22%3A%222023-05-05%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BCorey%2C%20R.%20A.%2C%20Baaden%2C%20M.%2C%20%26amp%3B%20Chavent%2C%20M.%20%282023%29.%20A%20brief%20history%20of%20visualizing%20membrane%20systems%20in%20molecular%20dynamics%20simulations.%20%26lt%3Bi%26gt%3BFrontiers%20in%20Bioinformatics%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306431%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306431%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20brief%20history%20of%20visualizing%20membrane%20systems%20in%20molecular%20dynamics%20simulations%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robin%20A.%22%2C%22lastName%22%3A%22Corey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthieu%22%2C%22lastName%22%3A%22Chavent%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222023-05-05%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306431%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T09%3A55%3A51Z%22%7D%7D%2C%7B%22key%22%3A%22S59E5EM5%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Lanrezac%20and%20Baaden%22%2C%22parsedDate%22%3A%222023-03-21%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BLanrezac%2C%20A.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282023%29.%20UNILIPID%2C%20a%20Methodology%20for%20Energetically%20Accurate%20Prediction%20of%20Protein%20Insertion%20into%20Implicit%20Membranes%20of%20Arbitrary%20Shape.%20%26lt%3Bi%26gt%3BMembranes%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306427%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306427%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22UNILIPID%2C%20a%20Methodology%20for%20Energetically%20Accurate%20Prediction%20of%20Protein%20Insertion%20into%20Implicit%20Membranes%20of%20Arbitrary%20Shape%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Lanrezac%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222023-03-21%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-04306427%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A07%3A07Z%22%7D%7D%2C%7B%22key%22%3A%22WVPL2HX9%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Zhang%20and%20Baaden%22%2C%22parsedDate%22%3A%222023-02%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BZhang%2C%20Y.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282023%29.%20Molecular%20Insights%20into%20Substrate%20Binding%20of%20the%20Outer%20Membrane%20Enzyme%20OmpT.%20%26lt%3Bi%26gt%3BCatalysts%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B13%26lt%3B%5C%2Fi%26gt%3B%282%29%2C%20214.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcatal13020214%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcatal13020214%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Molecular%20Insights%20into%20Substrate%20Binding%20of%20the%20Outer%20Membrane%20Enzyme%20OmpT%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yubo%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22The%20enzyme%20OmpT%20of%20the%20outer%20membrane%20of%20Escherichia%20coli%20shows%20proteolytic%20activity%20and%20cleaves%20peptides%20and%20proteins.%20Using%20molecular%20dynamics%20simulations%20in%20a%20fully%20hydrated%20lipid%20bilayer%20on%20a%20time%20scale%20of%20hundreds%20of%20nanoseconds%2C%20we%20draw%20a%20detailed%20atomic%20picture%20of%20substrate%20recognition%20in%20the%20OmpT-holo%20enzyme%20complex.%20Hydrogen%20bonds%20and%20salt%20bridges%20are%20essential%20for%20maintaining%20the%20integrity%20of%20the%20active%20site%20and%20play%20a%20central%20role%20for%20OmpT%20in%20recognizing%20its%20substrate.%20Electrostatic%20interactions%20are%20critical%20at%20all%20stages%20from%20approaching%20the%20substrate%20to%20docking%20at%20the%20active%20site.%20Computational%20alanine%20scanning%20based%20on%20the%20Molecular%20Mechanics%20Generalized%20Born%20Surface%20Area%20%28MM-GBSA%29%20approach%20confirms%20the%20importance%20of%20multiple%20residues%20in%20the%20active%20site%20that%20form%20salt%20bridges.%20The%20substrate%20fluctuates%20along%20the%20axis%20of%20the%20%5Cu03b2-barrel%2C%20which%20is%20associated%20with%20oscillations%20of%20the%20binding%20cleft%20formed%20by%20the%20residue%20pairs%20D210-H212%20and%20D83-D85.%20Principal%20component%20analysis%20suggests%20that%20substrate%20and%20protein%20movements%20are%20correlated.%20We%20observe%20the%20transient%20presence%20of%20putative%20catalytic%20water%20molecules%20near%20the%20active%20site%2C%20which%20may%20be%20involved%20in%20the%20nucleophilic%20attack%20on%20the%20cleavable%20peptide%20bond%20of%20the%20substrate.%22%2C%22date%22%3A%222023%5C%2F2%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.3390%5C%2Fcatal13020214%22%2C%22ISSN%22%3A%222073-4344%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.mdpi.com%5C%2F2073-4344%5C%2F13%5C%2F2%5C%2F214%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A00%3A53Z%22%7D%7D%2C%7B%22key%22%3A%22UYPFSJD9%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Lanrezac%20et%20al.%22%2C%22parsedDate%22%3A%222022-11%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BLanrezac%2C%20A.%2C%20Laurent%2C%20B.%2C%20Santuz%2C%20H.%2C%20F%26%23xE9%3Brey%2C%20N.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282022%29.%20Fast%20and%20Interactive%20Positioning%20of%20Proteins%20within%20Membranes.%20%26lt%3Bi%26gt%3BAlgorithms%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B15%26lt%3B%5C%2Fi%26gt%3B%2811%29%2C%20415.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fa15110415%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fa15110415%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Fast%20and%20Interactive%20Positioning%20of%20Proteins%20within%20Membranes%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Lanrezac%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benoist%22%2C%22lastName%22%3A%22Laurent%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hubert%22%2C%22lastName%22%3A%22Santuz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22F%5Cu00e9rey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22%281%29%20Background%3A%20We%20developed%20an%20algorithm%20to%20perform%20interactive%20molecular%20simulations%20%28IMS%29%20of%20protein%20alignment%20in%20membranes%2C%20allowing%20on-the-fly%20monitoring%20and%20manipulation%20of%20such%20molecular%20systems%20at%20various%20scales.%20%282%29%20Methods%3A%20UnityMol%2C%20an%20advanced%20molecular%20visualization%20software%3B%20MDDriver%2C%20a%20socket%20for%20data%20communication%3B%20and%20BioSpring%2C%20a%20Spring%20network%20simulation%20engine%2C%20were%20extended%20to%20perform%20IMS.%20These%20components%20are%20designed%20to%20easily%20communicate%20with%20each%20other%2C%20adapt%20to%20other%20molecular%20simulation%20software%2C%20and%20provide%20a%20development%20framework%20for%20adding%20new%20interaction%20models%20to%20simulate%20biological%20phenomena%20such%20as%20protein%20alignment%20in%20the%20membrane%20at%20a%20fast%20enough%20rate%20for%20real-time%20experiments.%20%283%29%20Results%3A%20We%20describe%20in%20detail%20the%20integration%20of%20an%20implicit%20membrane%20model%20for%20Integral%20Membrane%20Protein%20And%20Lipid%20Association%20%28IMPALA%29%20into%20our%20IMS%20framework.%20Our%20implementation%20can%20cover%20multiple%20levels%20of%20representation%2C%20and%20the%20degrees%20of%20freedom%20can%20be%20tuned%20to%20optimize%20the%20experience.%20We%20explain%20the%20validation%20of%20this%20model%20in%20an%20interactive%20and%20exhaustive%20search%20mode.%20%284%29%20Conclusions%3A%20Protein%20positioning%20in%20model%20membranes%20can%20now%20be%20performed%20interactively%20in%20real%20time.%22%2C%22date%22%3A%222022%5C%2F11%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.3390%5C%2Fa15110415%22%2C%22ISSN%22%3A%221999-4893%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.mdpi.com%5C%2F1999-4893%5C%2F15%5C%2F11%5C%2F415%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A08%3A50Z%22%7D%7D%2C%7B%22key%22%3A%22JRGGRFSG%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Baaden%22%2C%22parsedDate%22%3A%222022-08-01%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BBaaden%2C%20M.%20%282022%29.%20Deep%20inside%20molecules%20%26%23x2014%3B%20digital%20twins%20at%20the%20nanoscale.%20%26lt%3Bi%26gt%3BVirtual%20Reality%20%26amp%3B%20Intelligent%20Hardware%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B4%26lt%3B%5C%2Fi%26gt%3B%284%29%2C%20324%26%23x2013%3B341.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.vrih.2022.03.001%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.vrih.2022.03.001%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Deep%20inside%20molecules%20%5Cu2014%20digital%20twins%20at%20the%20nanoscale%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22Background%5CnDigital%20twins%20offer%20rich%20potential%20for%20exploration%20in%20virtual%20reality%20%28VR%29.%20Using%20interactive%20molecular%20simulation%20approaches%2C%20they%20enable%20a%20human%20operator%20to%20access%20the%20physical%20properties%20of%20molecular%20objects%20and%20to%20build%2C%20manipulate%2C%20and%20study%20their%20assemblies.%20Integrative%20modeling%20and%20drug%20design%20are%20important%20applications%20of%20this%20technology.%5CnMethods%5CnIn%20this%20study%2C%20head-mounted%20virtual%20reality%20displays%20connected%20to%20molecular%20simulation%20engines%20were%20used%20to%20create%20interactive%20and%20immersive%20digital%20twins.%20They%20were%20used%20to%20perform%20tasks%20relevant%20to%20specific%20use%20cases.%5CnResults%5CnThree%20areas%20were%20investigated%2C%20including%20model%20building%2C%20rational%20design%2C%20and%20tangible%20models.%20Here%2C%20we%20report%20several%20membrane-embedded%20systems%20of%20ion%20channels%2C%20viral%20components%2C%20and%20artificial%20water%20channels.%20We%20were%20able%20to%20improve%20and%20create%20molecular%20designs%20based%20on%20digital%20twins.%5CnConclusions%5CnThe%20molecular%20application%20domain%20offers%20great%20opportunities%2C%20and%20most%20of%20the%20technical%20and%20technological%20aspects%20have%20been%20solved.%20Wider%20adoption%20is%20expected%20once%20the%20onboarding%20of%20VR%20is%20simplified%20and%20the%20technology%20gains%20wider%20acceptance.%22%2C%22date%22%3A%222022-08-01%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.vrih.2022.03.001%22%2C%22ISSN%22%3A%222096-5796%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.sciencedirect.com%5C%2Fscience%5C%2Farticle%5C%2Fpii%5C%2FS2096579622000171%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A03%3A31Z%22%7D%7D%2C%7B%22key%22%3A%22TAKYC6EX%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Molza%20et%20al.%22%2C%22parsedDate%22%3A%222022%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMolza%2C%20A.-E.%2C%20Westermaier%2C%20Y.%2C%20Moutte%2C%20M.%2C%20Ducrot%2C%20P.%2C%20Danilowicz%2C%20C.%2C%20Godoy-Carter%2C%20V.%2C%20Prentiss%2C%20M.%2C%20Robert%2C%20C.%20H.%2C%20Baaden%2C%20M.%2C%20%26amp%3B%20Pr%26%23xE9%3Bvost%2C%20C.%20%282022%29.%20Building%20Biological%20Relevance%20Into%20Integrative%20Modelling%20of%20Macromolecular%20Assemblies.%20%26lt%3Bi%26gt%3BFrontiers%20in%20Molecular%20Biosciences%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03826944%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03826944%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Building%20Biological%20Relevance%20Into%20Integrative%20Modelling%20of%20Macromolecular%20Assemblies%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anne-Elisabeth%22%2C%22lastName%22%3A%22Molza%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yvonne%22%2C%22lastName%22%3A%22Westermaier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Magali%22%2C%22lastName%22%3A%22Moutte%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre%22%2C%22lastName%22%3A%22Ducrot%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Claudia%22%2C%22lastName%22%3A%22Danilowicz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Veronica%22%2C%22lastName%22%3A%22Godoy-Carter%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mara%22%2C%22lastName%22%3A%22Prentiss%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles%20H.%22%2C%22lastName%22%3A%22Robert%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chantal%22%2C%22lastName%22%3A%22Pr%5Cu00e9vost%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222022%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03826944%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T09%3A53%3A33Z%22%7D%7D%2C%7B%22key%22%3A%222J49EG39%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Spalvieri%20et%20al.%22%2C%22parsedDate%22%3A%222022%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BSpalvieri%2C%20D.%2C%20Mauviel%2C%20A.-M.%2C%20Lambert%2C%20M.%2C%20F%26%23xE9%3Brey%2C%20N.%2C%20Sacquin-Mora%2C%20S.%2C%20Chavent%2C%20M.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282022%29.%20Design%20%26%23x2013%3B%20a%20new%20way%20to%20look%20at%20old%20molecules.%20%26lt%3Bi%26gt%3BJournal%20of%20Integrative%20Bioinformatics%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B19%26lt%3B%5C%2Fi%26gt%3B%282%29%2C%2020220020.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1515%5C%2Fjib-2022-0020%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1515%5C%2Fjib-2022-0020%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Design%20%5Cu2013%20a%20new%20way%20to%20look%20at%20old%20molecules%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Davide%22%2C%22lastName%22%3A%22Spalvieri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anne-Marine%22%2C%22lastName%22%3A%22Mauviel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthieu%22%2C%22lastName%22%3A%22Lambert%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22F%5Cu00e9rey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Sacquin-Mora%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthieu%22%2C%22lastName%22%3A%22Chavent%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22We%20discuss%20how%20design%20enriches%20molecular%20science%2C%20particularly%20structural%20biology%20and%20bioinformatics.%20We%20present%20two%20use%20cases%2C%20one%20in%20academic%20practice%20and%20the%20other%20to%20design%20for%20outreach.%20The%20first%20case%20targets%20the%20representation%20of%20ion%20channels%20and%20their%20dynamic%20properties.%20In%20the%20second%2C%20we%20document%20a%20transition%20process%20from%20a%20research%20environment%20to%20general-purpose%20designs.%20Several%20testimonials%20from%20practitioners%20are%20given.%20By%20describing%20the%20design%20process%20of%20abstracted%20shapes%2C%20exploded%20views%20of%20molecular%20structures%2C%20motion-averaged%20slices%2C%20360-degree%20panoramic%20projections%2C%20and%20experiments%20with%20lit%20sphere%20shading%2C%20we%20document%20how%20designers%20help%20make%20scientific%20data%20accessible%20without%20betraying%20its%20meaning%2C%20and%20how%20a%20creative%20mind%20adds%20value%20over%20purely%20data-driven%20visualizations.%20A%20similar%20conclusion%20was%20drawn%20for%20public%20outreach%2C%20as%20we%20found%20that%20comic-book-style%20drawings%20are%20better%20suited%20for%20communicating%20science%20to%20a%20broad%20audience.%22%2C%22date%22%3A%222022%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1515%5C%2Fjib-2022-0020%22%2C%22ISSN%22%3A%221613-4516%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.ncbi.nlm.nih.gov%5C%2Fpmc%5C%2Farticles%5C%2FPMC9377703%5C%2F%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A00%3A08Z%22%7D%7D%2C%7B%22key%22%3A%228FDS5NV3%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Martinez%20and%20Baaden%22%2C%22parsedDate%22%3A%222021-06%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMartinez%2C%20X.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282021%29.%20UnityMol%20prototype%20for%20FAIR%20sharing%20of%20molecular-%20visualization%20experiences%3A%20from%20pictures%20in%20the%20cloud%20to%20collaborative%20virtual%20reality%20exploration%20in%20immersive%203D%20environments.%20%26lt%3Bi%26gt%3BActa%20Crystallographica%20Section%20D%26%23x202F%3B%3A%20Structural%20Biology%20%5B1993-...%5D%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02944943%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02944943%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22UnityMol%20prototype%20for%20FAIR%20sharing%20of%20molecular-%20visualization%20experiences%3A%20from%20pictures%20in%20the%20cloud%20to%20collaborative%20virtual%20reality%20exploration%20in%20immersive%203D%20environments%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Martinez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021-06%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02944943%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A06%3A24Z%22%7D%7D%2C%7B%22key%22%3A%22Y8CY9Q7F%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Hardiagon%20et%20al.%22%2C%22parsedDate%22%3A%222021-05-14%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BHardiagon%2C%20A.%2C%20Murail%2C%20S.%2C%20Huang%2C%20L.-B.%2C%20van%20der%20Lee%2C%20A.%2C%20Sterpone%2C%20F.%2C%20Barboiu%2C%20M.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282021%29.%20Molecular%20dynamics%20simulations%20reveal%20statistics%20and%20microscopic%20mechanisms%20of%20water%20permeation%20in%20membrane-embedded%20artificial%20water%20channel%20nanoconstructs.%20%26lt%3Bi%26gt%3BThe%20Journal%20of%20Chemical%20Physics%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B154%26lt%3B%5C%2Fi%26gt%3B%2818%29%2C%20184102.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0044360%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0044360%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Molecular%20dynamics%20simulations%20reveal%20statistics%20and%20microscopic%20mechanisms%20of%20water%20permeation%20in%20membrane-embedded%20artificial%20water%20channel%20nanoconstructs%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Arthur%22%2C%22lastName%22%3A%22Hardiagon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Samuel%22%2C%22lastName%22%3A%22Murail%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Li-Bo%22%2C%22lastName%22%3A%22Huang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Arie%22%2C%22lastName%22%3A%22van%20der%20Lee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabio%22%2C%22lastName%22%3A%22Sterpone%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mihail%22%2C%22lastName%22%3A%22Barboiu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22Understanding%20water%20transport%20mechanisms%20at%20the%20nanoscale%20level%20remains%20a%20challenge%20for%20theoretical%20chemical%20physics.%20Major%20advances%20in%20chemical%20synthesis%20have%20allowed%20us%20to%20discover%20new%20artificial%20water%20channels%2C%20rivaling%20with%20or%20even%20surpassing%20water%20conductance%20and%20selectivity%20of%20natural%20protein%20channels.%20In%20order%20to%20interpret%20experimental%20features%20and%20understand%20microscopic%20determinants%20for%20performance%20improvements%2C%20numerical%20approaches%20based%20on%20all-atom%20molecular%20dynamics%20simulations%20and%20enhanced%20sampling%20methods%20have%20been%20proposed.%20In%20this%20study%2C%20we%20quantify%20the%20influence%20of%20microscopic%20observables%2C%20such%20as%20channel%20radius%20and%20hydrogen%20bond%20connectivity%2C%20and%20of%20meso-scale%20features%2C%20such%20as%20the%20size%20of%20self-assembly%20blocks%2C%20on%20the%20permeation%20rate%20of%20a%20self-assembled%20nanocrystal-like%20artificial%20water%20channel.%20Although%20the%20absolute%20permeation%20rate%20extrapolated%20from%20these%20simulations%20is%20overestimated%20by%20one%20order%20of%20magnitude%20compared%20to%20the%20experimental%20measurement%2C%20the%20detailed%20analysis%20of%20several%20observed%20conductive%20patterns%20in%20large%20assemblies%20opens%20new%20pathways%20to%20scalable%20membranes%20with%20enhanced%20water%20conductance%20for%20the%20future%20design.%22%2C%22date%22%3A%222021-05-14%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1063%5C%2F5.0044360%22%2C%22ISSN%22%3A%221089-7690%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T07%3A44%3A55Z%22%7D%7D%2C%7B%22key%22%3A%22Z3VV8AAM%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Lanrezac%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BLanrezac%2C%20A.%2C%20F%26%23xE9%3Brey%2C%20N.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282021%29.%20Wielding%20the%20power%20of%20interactive%20molecular%20simulations.%20%26lt%3Bi%26gt%3BWiley%20Interdisciplinary%20Reviews%3A%20Computational%20Molecular%20Science%26lt%3B%5C%2Fi%26gt%3B.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03447181%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03447181%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Wielding%20the%20power%20of%20interactive%20molecular%20simulations%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Lanrezac%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22F%5Cu00e9rey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-03447181%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A05%3A41Z%22%7D%7D%2C%7B%22key%22%3A%22XFI3HIKF%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22lastModifiedByUser%22%3A%7B%22id%22%3A6615510%2C%22username%22%3A%22Bchris104%22%2C%22name%22%3A%22%22%2C%22links%22%3A%7B%22alternate%22%3A%7B%22href%22%3A%22https%3A%5C%2F%5C%2Fwww.zotero.org%5C%2Fbchris104%22%2C%22type%22%3A%22text%5C%2Fhtml%22%7D%7D%7D%2C%22creatorSummary%22%3A%22Martinez%20and%20Baaden%22%2C%22parsedDate%22%3A%222020-02%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMartinez%2C%20X.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282020%29.%20Scruter%20les%20mol%26%23xE9%3Bcules%20en%20r%26%23xE9%3Balit%26%23xE9%3B%20virtuelle%2C%20pour%20quoi%20faire%26%23x202F%3B%3F%20%26lt%3Bi%26gt%3BL%26%23x2019%3BActualit%26%23xE9%3B%20Chimique%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B448%26lt%3B%5C%2Fi%26gt%3B%2C%2023%26%23x2013%3B26.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02946000%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02946000%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Scruter%20les%20mol%5Cu00e9cules%20en%20r%5Cu00e9alit%5Cu00e9%20virtuelle%2C%20pour%20quoi%20faire%20%3F%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Martinez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22Molecular%20representations%20are%20taking%20an%20important%20role%20in%20communicating%20ideas%2C%20in%20generating%20new%20hypotheses%20on%20biological%20mechanisms%20and%20in%20analysing%20molecular%20simulations.%20However%2C%20the%20current%20devices%20used%20to%20observe%20and%20manipulate%20these%20molecular%20systems%20are%20typically%20limited%20to%20the%20two%20dimensions%20of%20the%20computer%20screen%20combined%20with%20a%20keyboard%20and%20a%20mouse%20offering%20limited%20interaction%20capabilities.%20Nowadays%2C%20virtual%20reality%20headsets%20offer%20a%20more%20performant%20and%20accessible%20solution.%20However%2C%20adaptations%20are%20necessary%20to%20fully%20benefit%20from%20the%20advantages%20of%20using%20virtual%20reality%20for%20scientific%20visualisation.%20This%20paper%20presents%20a%20few%20examples%20implemented%20with%20the%20UnityMol%20software.%20In%20addition%20to%20immediate%20applications%20in%20teaching%2C%20the%20paradigm%20shift%20in%20interaction%20and%20the%20increased%20depth%20perception%20and%20shape%20comprehension%20of%20biological%20molecules%20are%20already%20easing%20the%20grasp%20of%20these%20complex%20systems%20and%20will%20certainly%20lead%20to%20the%20discovery%20of%20new%20scientific%20knowledge.%22%2C%22date%22%3A%222020-02%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fhal.science%5C%2Fhal-02946000%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%5D%2C%22dateModified%22%3A%222024-12-11T10%3A01%3A36Z%22%7D%7D%2C%7B%22key%22%3A%224CW8KTMZ%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Martinez%20et%20al.%22%2C%22parsedDate%22%3A%222020%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMartinez%2C%20X.%2C%20Hardiagon%2C%20A.%2C%20Santuz%2C%20H.%2C%20Murail%2C%20S.%2C%20Barboiu%2C%20M.%2C%20Sterpone%2C%20F.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282020%29.%20Using%20Computer%20Simulations%20and%20Virtual%20Reality%20to%20Understand%2C%20Design%20and%20Optimize%20Artificial%20Water%20Channels.%20In%20S.%20Piotto%2C%20S.%20Concilio%2C%20L.%20Sessa%2C%20%26amp%3B%20F.%20Rossi%20%28Eds.%29%2C%20%26lt%3Bi%26gt%3BAdvances%20in%20Bionanomaterials%20II%26lt%3B%5C%2Fi%26gt%3B%20%28pp.%2078%26%23x2013%3B99%29.%20Springer%20International%20Publishing.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2F978-3-030-47705-9_8%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2F978-3-030-47705-9_8%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22conferencePaper%22%2C%22title%22%3A%22Using%20Computer%20Simulations%20and%20Virtual%20Reality%20to%20Understand%2C%20Design%20and%20Optimize%20Artificial%20Water%20Channels%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Martinez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Arthur%22%2C%22lastName%22%3A%22Hardiagon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hubert%22%2C%22lastName%22%3A%22Santuz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Samuel%22%2C%22lastName%22%3A%22Murail%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mihail%22%2C%22lastName%22%3A%22Barboiu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabio%22%2C%22lastName%22%3A%22Sterpone%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Stefano%22%2C%22lastName%22%3A%22Piotto%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Simona%22%2C%22lastName%22%3A%22Concilio%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Lucia%22%2C%22lastName%22%3A%22Sessa%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Federico%22%2C%22lastName%22%3A%22Rossi%22%7D%5D%2C%22abstractNote%22%3A%22In%20biology%2C%20metabolite%20transport%20across%20cell%20membranes%20occurs%20through%20natural%20channels%20and%20pores.%20Artificial%20ion-channel%20architectures%20represent%20potential%20mimics%20of%20natural%20ionic%20conduction.%20Many%20such%20systems%20were%20produced%20leading%20to%20a%20remarkable%20set%20of%20alternative%20artificial%20ion-channels.%20Far%20less%20advances%20were%20achieved%20in%20the%20area%20of%20synthetic%20biomimetic%20water%20channels%2C%20even%20though%20they%20could%20improve%20our%20understanding%20of%20the%20natural%20function%20of%20protein%20channels%20and%20may%20provide%20new%20strategies%20to%20generate%20highly%20selective%2C%20advanced%20water%20purification%20systems.%20Most%20realizations%20have%20used%20the%20selectivity%20components%20of%20natural%20protein%20channels%20embedded%20in%20artificial%20systems.%20Such%20biomolecules%20provide%20building%20blocks%20to%20constitute%20highly%20selective%20membrane-spanning%20water%20transport%20architectures.%20The%20simplification%20of%20such%20compounds%2C%20while%20preserving%20the%20high%20conduction%20activity%20of%20natural%20macromolecules%2C%20lead%20to%20fully%20synthetic%20artificial%20biomimetic%20channels.%20These%20simplified%20systems%20offer%20a%20particular%20chance%20to%20understand%20mechanistic%20and%20structural%20behaviors%2C%20providing%20rationales%20to%20engineer%20better%20artificial%20water-channels.%20Here%20we%20focus%20on%20computer%20simulations%20as%20a%20tool%20to%20complement%20experiment%20in%20understanding%20the%20properties%20of%20such%20systems%20with%20the%20aim%20to%20rationalize%20important%20concepts%2C%20design%20and%20optimize%20better%20compounds.%20Molecular%20dynamics%20simulations%20combined%20with%20advanced%20visual%20scrutiny%20thereof%20are%20central%20to%20such%20an%20approach.%20Novel%20technologies%20such%20as%20virtual%20reality%20headsets%20and%20stereoscopic%20large-scale%20display%20walls%20offer%20immersive%20collaborative%20insight%20into%20the%20complex%20mechanisms%20underlying%20artificial%20water%20channel%20function.%22%2C%22date%22%3A%222020%22%2C%22proceedingsTitle%22%3A%22Advances%20in%20Bionanomaterials%20II%22%2C%22conferenceName%22%3A%22%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1007%5C%2F978-3-030-47705-9_8%22%2C%22ISBN%22%3A%22978-3-030-47705-9%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T07%3A45%3A38Z%22%7D%7D%2C%7B%22key%22%3A%22S7BBLV88%22%2C%22library%22%3A%7B%22id%22%3A5511665%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Maes%20et%20al.%22%2C%22parsedDate%22%3A%222018%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%202%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMaes%2C%20A.%2C%20Martinez%2C%20X.%2C%20Druart%2C%20K.%2C%20Laurent%2C%20B.%2C%20Gu%26%23xE9%3Bgan%2C%20S.%2C%20Marchand%2C%20C.%20H.%2C%20Lemaire%2C%20S.%20D.%2C%20%26amp%3B%20Baaden%2C%20M.%20%282018%29.%20MinOmics%2C%20an%20Integrative%20and%20Immersive%20Tool%20for%20Multi-Omics%20Analysis.%20%26lt%3Bi%26gt%3BJournal%20of%20Integrative%20Bioinformatics%26lt%3B%5C%2Fi%26gt%3B%2C%20%26lt%3Bi%26gt%3B15%26lt%3B%5C%2Fi%26gt%3B%282%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1515%5C%2Fjib-2018-0006%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1515%5C%2Fjib-2018-0006%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22MinOmics%2C%20an%20Integrative%20and%20Immersive%20Tool%20for%20Multi-Omics%20Analysis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexandre%22%2C%22lastName%22%3A%22Maes%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Martinez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karen%22%2C%22lastName%22%3A%22Druart%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benoist%22%2C%22lastName%22%3A%22Laurent%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%22%2C%22lastName%22%3A%22Gu%5Cu00e9gan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christophe%20H.%22%2C%22lastName%22%3A%22Marchand%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22St%5Cu00e9phane%20D.%22%2C%22lastName%22%3A%22Lemaire%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baaden%22%7D%5D%2C%22abstractNote%22%3A%22Proteomic%20and%20transcriptomic%20technologies%20resulted%20in%20massive%20biological%20datasets%2C%20their%20interpretation%20requiring%20sophisticated%20computational%20strategies.%20Efficient%20and%20intuitive%20real-time%20analysis%20remains%20challenging.%20We%20use%20proteomic%20data%20on%201417%20proteins%20of%20the%20green%20microalga%20Chlamydomonas%20reinhardtii%20to%20investigate%20physicochemical%20parameters%20governing%20selectivity%20of%20three%20cysteine-based%20redox%20post%20translational%20modifications%20%28PTM%29%3A%20glutathionylation%20%28SSG%29%2C%20nitrosylation%20%28SNO%29%20and%20disulphide%20bonds%20%28SS%29%20reduced%20by%20thioredoxins.%20We%20aim%20to%20understand%20underlying%20molecular%20mechanisms%20and%20structural%20determinants%20through%20integration%20of%20redox%20proteome%20data%20from%20gene-%20to%20structural%20level.%20Our%20interactive%20visual%20analytics%20approach%20on%20an%208.3%20m2%20display%20wall%20of%2025%20MPixel%20resolution%20features%20stereoscopic%20three%20dimensions%20%283D%29%20representation%20performed%20by%20UnityMol%20WebGL.%20Virtual%20reality%20headsets%20complement%20the%20range%20of%20usage%20configurations%20for%20fully%20immersive%20tasks.%20Our%20experiments%20confirm%20that%20fast%20access%20to%20a%20rich%20cross-linked%20database%20is%20necessary%20for%20immersive%20analysis%20of%20structural%20data.%20We%20emphasize%20the%20possibility%20to%20display%20complex%20data%20structures%20and%20relationships%20in%203D%2C%20intrinsic%20to%20molecular%20structure%20visualization%2C%20but%20less%20common%20for%20omics-network%20analysis.%20Our%20setup%20is%20powered%20by%20MinOmics%2C%20an%20integrated%20analysis%20pipeline%20and%20visualization%20framework%20dedicated%20to%20multi-omics%20analysis.%20MinOmics%20integrates%20data%20from%20various%20sources%20into%20a%20materialized%20physical%20repository.%20We%20evaluate%20its%20performance%2C%20a%20design%20criterion%20for%20the%20framework.%22%2C%22date%22%3A%222018%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1515%5C%2Fjib-2018-0006%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.degruyter.com%5C%2Fview%5C%2Fj%5C%2Fjib.ahead-of-print%5C%2Fjib-2018-0006%5C%2Fjib-2018-0006.xml%22%2C%22collections%22%3A%5B%2282TPS5CH%22%2C%22KUXFT82A%22%2C%224DATDKWW%22%5D%2C%22dateModified%22%3A%222024-12-11T07%3A45%3A17Z%22%7D%7D%5D%7D
Laurent, B., Lanrezac, A., Santuz, H., Ferey, N., Delalande, O., & Baaden, M. (2025). BioSpring : An elastic network framework for interactive exploration of macromolecular mechanics. Protein Science, 34(5), e70130. https://doi.org/10.1002/pro.70130
Versini, R., Sritharan, S., Aykac Fas, B., Tubiana, T., Aimeur, S. Z., Henri, J., Erard, M., Nüsse, O., Andreani, J., Baaden, M., Fuchs, P., Galochkina, T., Chatzigoulas, A., Cournia, Z., Santuz, H., Sacquin-Mora, S., & Taly, A. (2024). A Perspective on the Prospective Use of AI in Protein Structure Prediction. Journal of Chemical Information and Modeling, 64(1), 26–41. https://doi.org/10.1021/acs.jcim.3c01361
Darbar, R., Santuz, H., Taly, A., & Baaden, M. (2024). GazeMolVR: Sharing Eye-Gaze Cues in a Collaborative VR Environment for Molecular Visualization. Proceedings of the International Conference on Mobile and Ubiquitous Multimedia, 7–23. https://doi.org/10.1145/3701571.3701599
Kuťák, D., Vázquez, P., Isenberg, T., Krone, M., Baaden, M., Byška, J., Kozlíková, B., & Miao, H. (2023). State of the Art of Molecular Visualization in Immersive Virtual Environments. Computer Graphics Forum. https://inria.hal.science/hal-04006531
Gagelin, A., Largeau, C., Masscheleyn, S., Piel, M. S., Calderón-Mora, D., Bouillaud, F., Hénin, J., & Miroux, B. (2023). Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling. Nature Communications, 14(1), 2594. https://doi.org/10.1038/s41467-023-38219-9
Corey, R. A., Baaden, M., & Chavent, M. (2023). A brief history of visualizing membrane systems in molecular dynamics simulations. Frontiers in Bioinformatics. https://hal.science/hal-04306431
Lanrezac, A., & Baaden, M. (2023). UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. Membranes. https://hal.science/hal-04306427
Zhang, Y., & Baaden, M. (2023). Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT. Catalysts, 13(2), 214. https://doi.org/10.3390/catal13020214
Lanrezac, A., Laurent, B., Santuz, H., Férey, N., & Baaden, M. (2022). Fast and Interactive Positioning of Proteins within Membranes. Algorithms, 15(11), 415. https://doi.org/10.3390/a15110415
Baaden, M. (2022). Deep inside molecules — digital twins at the nanoscale. Virtual Reality & Intelligent Hardware, 4(4), 324–341. https://doi.org/10.1016/j.vrih.2022.03.001
Molza, A.-E., Westermaier, Y., Moutte, M., Ducrot, P., Danilowicz, C., Godoy-Carter, V., Prentiss, M., Robert, C. H., Baaden, M., & Prévost, C. (2022). Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. https://hal.science/hal-03826944
Spalvieri, D., Mauviel, A.-M., Lambert, M., Férey, N., Sacquin-Mora, S., Chavent, M., & Baaden, M. (2022). Design – a new way to look at old molecules. Journal of Integrative Bioinformatics, 19(2), 20220020. https://doi.org/10.1515/jib-2022-0020
Martinez, X., & Baaden, M. (2021). UnityMol prototype for FAIR sharing of molecular- visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments. Acta Crystallographica Section D : Structural Biology [1993-...]. https://hal.science/hal-02944943
Hardiagon, A., Murail, S., Huang, L.-B., van der Lee, A., Sterpone, F., Barboiu, M., & Baaden, M. (2021). Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs. The Journal of Chemical Physics, 154(18), 184102. https://doi.org/10.1063/5.0044360
Lanrezac, A., Férey, N., & Baaden, M. (2021). Wielding the power of interactive molecular simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science. https://hal.science/hal-03447181
Martinez, X., & Baaden, M. (2020). Scruter les molécules en réalité virtuelle, pour quoi faire ? L’Actualité Chimique, 448, 23–26. https://hal.science/hal-02946000
Martinez, X., Hardiagon, A., Santuz, H., Murail, S., Barboiu, M., Sterpone, F., & Baaden, M. (2020). Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels. In S. Piotto, S. Concilio, L. Sessa, & F. Rossi (Eds.), Advances in Bionanomaterials II (pp. 78–99). Springer International Publishing. https://doi.org/10.1007/978-3-030-47705-9_8
Maes, A., Martinez, X., Druart, K., Laurent, B., Guégan, S., Marchand, C. H., Lemaire, S. D., & Baaden, M. (2018). MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. Journal of Integrative Bioinformatics, 15(2). https://doi.org/10.1515/jib-2018-0006