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dc.contributor.authorHermosilla, Pedro
dc.contributor.authorEstrada, Jorge
dc.contributor.authorGuallar, Víctor
dc.contributor.authorRopinski, Timo
dc.contributor.authorVinacua Pla, Álvaro
dc.contributor.authorVázquez Alcocer, Pere Pau
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament de Ciències de la Computació
dc.date.accessioned2016-12-15T11:18:25Z
dc.date.available2016-12-15T11:18:25Z
dc.date.issued2017-01-01
dc.identifier.citationHermosilla, P., Estrada, J., Guallar, V., Ropinski, T., Vinacua, A., Vázquez, P. Physics-based visual characterization of molecular interaction forces. "IEEE transactions on visualization and computer graphics", 1 Gener 2017, vol. 23, núm. 1, p. 731-740.
dc.identifier.issn1077-2626
dc.identifier.urihttp://hdl.handle.net/2117/98321
dc.description.abstractMolecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. 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: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.
dc.format.extent10 p.
dc.language.isoeng
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica
dc.subjectÀrees temàtiques de la UPC::Informàtica::Infografia
dc.subject.lcshProtein research
dc.subject.lcshThree-dimensional display systems
dc.subject.lcshInformation visualization
dc.subject.otherVisualization
dc.subject.otherThree-dimensional displays
dc.subject.otherComputational modeling
dc.subject.otherTwo dimensional displays
dc.subject.otherProteins
dc.subject.otherDrugs
dc.subject.otherData visualization
dc.titlePhysics-based visual characterization of molecular interaction forces
dc.typeArticle
dc.subject.lemacProteïnes -- Investigació
dc.subject.lemacVisualització tridimensional (Informàtica)
dc.subject.lemacVisualització de la informació
dc.contributor.groupUniversitat Politècnica de Catalunya. ViRVIG - Grup de Recerca en Visualització, Realitat Virtual i Interacció Gràfica
dc.identifier.doi10.1109/TVCG.2016.2598825
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://ieeexplore.ieee.org/document/7539331/
dc.rights.accessOpen Access
local.identifier.drac19342547
dc.description.versionPostprint (author's final draft)
local.citation.authorHermosilla, P.; Estrada, J.; Guallar, V.; Ropinski, T.; Vinacua, A.; Vázquez, P.
local.citation.publicationNameIEEE transactions on visualization and computer graphics
local.citation.volume23
local.citation.number1
local.citation.startingPage731
local.citation.endingPage740


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