Haptic Rendering Algorithm for Biomolecular Docking with Torque Force

Hou, Xiyuan; Sourina, Olga

doi:10.1109/cw.2010.59

Cited by 8 publications

(7 citation statements)

References 27 publications

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“…Their brute force calculations, however, did not account for all interatomic VDW interactions, but only for those involving the surface atoms of the molecules. Hou and Sourina 31 and Sourina et. al.…”

Section: Previous Workmentioning

confidence: 95%

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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Section: Previous Workmentioning

confidence: 95%

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

2014

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“…The “correct” pose should result in a high score. Interactive systems put the user in charge of the docking process, allowing them to use their knowledge and intuition to find a docked pose. , …”

Section: Introductionmentioning

confidence: 99%

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility

Matthews

Kitao

Laycock

et al. 2019

J. Chem. Inf. Model.

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Haptic-assisted interactive docking tools immerse the user in an environment where intuition and knowledge can be used to help guide the docking process. Here we present such a tool where the user "holds" a rigid ligand via a haptic device through which they feel interaction forces with a flexible receptor biomolecule. To ensure forces transmitted through the haptic device are smooth and stable, they must be updated at a rate greater than 500 Hz. Due to this time constraint, the majority of haptic docking tools do not attempt to model the conformational changes that would occur when molecules interact during binding. Our haptic-assisted docking tool, "Haptimol FlexiDock", models a receptor's conformational response to forces of interaction with a ligand whilst maintaining the required haptic refresh rate. In order to model receptor flexibility we use the method of linear response for which we determine the variance-covariance matrix of atomic fluctuations from the trajectory of an explicit-solvent Molecular Dynamics simulation of the ligand-free receptor molecule. Key to satisfying the time constraint is an eigenvector decomposition of the variance-covariance matrix which enables a good approximation to the conformational response of the receptor to be calculated rapidly. This exploits a feature of protein dynamics whereby most fluctuation occurs within a relatively small subspace. The method is demonstrated on Glutamine Binding Protein in interaction with glutamine, and Maltose Binding Protein in interaction with maltose. For both proteins the movement that occurs when the ligand is docked near to its binding site matches the experimentally determined movement well. It is thought that this tool will be particularly useful for structure-based drug design.

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“…Thus, the user could have a possibility to act in the game in a similar way as in the real world. Using technologies such as EEG reading devices and haptic devices allow proposing new approaches in serious game design and development [Wang et al 2011;Hou and Sourina 2010;Palluel-Germain et al 2007;Minchev et al 2009]. …”

Section: Introductionmentioning

confidence: 99%

Emotion-enabled haptic-based serious game for post stroke rehabilitation

Hou

Sourina

2013

Proceedings of the 19th ACM Symposium on Virtual Reality Software and Technology

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In this paper, we propose and develop a novel adaptive haptic-based serious game for post stroke rehabilitation. Real-time patients emotions monitoring based on the Electroencephalogram (EEG) is used as an additional game control. A subject-dependent algorithm recognizing negative and positive emotions from EEG is integrated. Force feedback is proposed and implemented in the game. The proposed EEG-enabled haptic-based serious game could help to promote rehabilitation of the patients with motor deficits after stroke. Such games could be used by the patients for post stroke rehabilitation even at home convenience without a nurse presence.

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Haptic Rendering Algorithm for Biomolecular Docking with Torque Force

Cited by 8 publications

References 27 publications

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

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

Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility

Emotion-enabled haptic-based serious game for post stroke rehabilitation

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