Dataset Information

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

ABSTRACT: The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC VIVE and the OCULUS RIFT utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

SUBMITTER: Ratamero EM

PROVIDER: S-EPMC6028860 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Publications

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

Ratamero Erick Martins EM Bellini Dom D Dowson Christopher G CG Römer Rudolf A RA

Journal of computer-aided molecular design 20180607 6

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful ...[more]

PMID: 29882064

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Project description:BackgroundStroke is a frequent cause of adult disability that can lead to enduring impairments. However, given the life-long plasticity of the brain one could assume that recovery could be facilitated by the harnessing of mechanisms underlying neuronal reorganization. Currently it is not clear how this reorganization can be mobilized. Novel technology based neurorehabilitation techniques hold promise to address this issue. Here we describe a Virtual Reality (VR) based system, the Rehabilitation Gaming System (RGS) that is based on a number of hypotheses on the neuronal mechanisms underlying recovery, the structure of training and the role of individualization. We investigate the psychometrics of the RGS in stroke patients and healthy controls.MethodsWe describe the key components of the RGS and the psychometrics of one rehabilitation scenario called Spheroids. We performed trials with 21 acute/subacute stroke patients and 20 healthy controls to study the effect of the training parameters on task performance. This allowed us to develop a Personalized Training Module (PTM) for online adjustment of task difficulty. In addition, we studied task transfer between physical and virtual environments. Finally, we assessed the usability and acceptance of the RGS as a rehabilitation tool.ResultsWe show that the PTM implemented in RGS allows us to effectively adjust the difficulty and the parameters of the task to the user by capturing specific features of the movements of the arms. The results reported here also show a consistent transfer of movement kinematics between physical and virtual tasks. Moreover, our usability assessment shows that the RGS is highly accepted by stroke patients as a rehabilitation tool.ConclusionsWe introduce a novel VR based paradigm for neurorehabilitation, RGS, which combines specific rehabilitative principles with a psychometric evaluation to provide a personalized and automated training. Our results show that the RGS effectively adjusts to the individual features of the user, allowing for an unsupervised deployment of individualized rehabilitation protocols.

Project description:Feedback outcomes are generally classified into positive and negative feedback. People often predict a feedback outcome with information that is based on both objective facts and uncertain subjective information, such as a mood. For example, if an action leads to good results consecutively, people performing the action overestimate the behavioral result of the next action. In electroencephalogram measurements, negative feedback evokes negative potential, called feedback negativity, and positive feedback evokes positive potential, called reward positivity. The present study investigated the relationship between the degree of the mood caused by the feedback outcome and the error-related brain potentials. We measured the electroencephalogram activity while the participants played a virtual reality shooting game. The experimental task was to shoot down a cannonball flying toward the player using a handgun. The task difficulty was determined from the size and curve of the flying cannonball. These gaming parameters affected the outcome probability of shooting the target in the game. We also implemented configurations in the game, such as the player's life points and play times. These configurations affected the outcome magnitude of shooting the target in the game. Moreover, we used the temporal accuracy of shooting in the game as the parameter of the mood. We investigated the relationship between these experimental features and the event-related potentials using the single-trial-based linear mixed-effects model analysis. The feedback negativity was observed at an error trial, and its amplitude was modulated with the outcome probability and the mood. Conversely, reward positivity was observed at hit trials, but its amplitude was modulated with the outcome probability and outcome magnitude. This result suggests that feedback negativity is enhanced according to not only the feedback probability but also the mood that was changed depending on the temporal gaming outcome.

Dataset Information

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

Publications

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

Similar Datasets

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