Multisensory VR interaction for protein-docking in the CoRSAIRe project

Férey, Nicolas; Nelson, Julien; Martin, Christine; Picinali, Lorenzo; Bouyer, Guillaume; Tek, Alex; Bourdot, Patrick; Burkhardt, Jean‐Marie; Katz, Brian F. G.; Ammi, Mehdi; Etchebest, Catherine; Autin, Ludovic

doi:10.1007/s10055-009-0136-z

Cited by 43 publications

(30 citation statements)

References 37 publications

(15 reference statements)

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“…Indeed, previous research on immersive 3D environments has shown that most benefits associated with such are demonstrated with inherently spatial tasks such as protein folding (Férey, Nelson, Martin et al, 2009). …”

Section: Discussionmentioning

confidence: 99%

A cognitive prosthesis for complex decision-making

et al. 2017

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While simple heuristics can be ecologically rational and effective in naturalistic decision making contexts, complex situations require analytical decision making strategies, hypothesis-testing and learning. Sub-optimal decision strategies -using simplified as opposed to analytic decision rules -have been reported in domains such as healthcare, military operational planning, and government policy making. We investigate the potential of a computational toolkit called "IMAGE" to improve decision-making by developing structural knowledge and increasing understanding of complex situations. IMAGE is tested within the context of a complex military convoy management task through (a) interactive simulations, and (b) visualization and knowledge representation capabilities. We assess the usefulness of two versions of IMAGE (desktop and immersive) compared to a baseline. Results suggest that the prosthesis helped analysts in making better decisions, but failed to increase their structural knowledge about the situation once the cognitive prosthesis is removed.

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Section: Discussionmentioning

confidence: 99%

A cognitive prosthesis for complex decision-making

et al. 2017

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“…Touch is also exploited in systems that utilize tangible physical models [ 6 ] that may be augmented virtually [ 7 ] and which have shown promise in enhancing student learning [ 8 ]. Beyond touch, a variety of sensory channels related to visual and audio feedback may be used to enhance the immersive effect, and preliminary applications of such integrated methods have occurred in the context of docking problems [ 9 ]. The design and utilization of efficient and effective strategies for interaction with a molecular simulation relies on careful consideration of methods developed within the field of human-computer interaction.…”

Section: Virtual and Augmented Reality And Immersive Molecular Simulamentioning

confidence: 99%

Molecular simulations and visualization: introduction and overview

Hirst¹,

Glowacki²,

Baaden³

2014

Faraday Discuss.

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“…al. 30 calculated the docking forces using a force grid for the electrostatic contribution and a brute force approach for the VDW contribution. Their brute force calculations, however, did not account for all interatomic VDW interactions, but only for those involving the surface atoms of the molecules.…”

Section: Previous Workmentioning

confidence: 99%

A real-time proximity querying algorithm for haptic-based molecular docking

2014

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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, forcefeedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware.

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Multisensory VR interaction for protein-docking in the CoRSAIRe project

Cited by 43 publications

References 37 publications

A cognitive prosthesis for complex decision-making

A cognitive prosthesis for complex decision-making

Molecular simulations and visualization: introduction and overview

A real-time proximity querying algorithm for haptic-based molecular docking

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