Computing power revolution and new algorithms: GP-GPUs, clouds and more: general discussion

McIntosh-Smith,; Tchertanov,; Nerukh,; Stone,; Baaden,; Hayward,; Glowacki,; Olson, Matthew R.; Zoppè,; Петров,; Hall,; Reiher,; Brancale,; Haag,; O'Donoghue,; Brooks,; Raffin,; Iakovou,; Chavent,; Sánchez, Nicolás. Montés; Baker,; Thomas, D. S.; Woods, Roger; Hirst,

doi:10.1039/c4fd90021a

Cited by 8 publications

(7 citation statements)

References 1 publication

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“…Haptics-assisted interactive docking systems provide a visuohaptic representation of the molecular world, while enabling the user to interact with the virtual molecules, and perform a knowledge-guided search and selection of the final binding pose. They offer an immersive virtual learning environment for the study of molecular docking, and a test bed for exploring new ideas and hypotheses (e.g., whether electrostatic steering is involved in the process). Although they are not able to search a large number of docking pairs as in automated docking, − they do allow the user to focus the search and to potentially improve the result based on their knowledge and expertise. , For example, in virtual screening they can assist experts to improve upon or reject the high-scoring docking conformations identified by automated methods. , Unlike automated docking in which implicit solvent force fields and molecular flexibility are sometimes included, most of the existing interactive docking applications are limited to rigid-molecule models with interaction forces calculated as sums of pairwise distance-dependent interactions.…”

Section: Introductionmentioning

confidence: 99%

“…They offer an immersive virtual learning environment for the study of molecular docking, and a test bed for exploring new ideas and hypotheses (e.g., whether electrostatic steering is involved in the process). Although they are not able to search a large number of docking pairs as in automated docking, − they do allow the user to focus the search and to potentially improve the result based on their knowledge and expertise. , For example, in virtual screening they can assist experts to improve upon or reject the high-scoring docking conformations identified by automated methods. , Unlike automated docking in which implicit solvent force fields and molecular flexibility are sometimes included, most of the existing interactive docking applications are limited to rigid-molecule models with interaction forces calculated as sums of pairwise distance-dependent interactions. The fundamental reason for this is the demanding refresh rate of 500 Hz to 1 kHz which is required due to the sensitivity of the human haptic system. − Failure to meet this rate can result in vibrations and force discontinuities that can limit the practical use of such a system.…”

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

“…19,20 For example, in virtual screening they can assist experts to improve upon or reject the highscoring docking conformations identified by automated methods. 14,21 Unlike automated docking in which implicit solvent force fields and molecular flexibility are sometimes included, most of the existing interactive docking applications are limited to rigid-molecule models with interaction forces calculated as sums of pairwise distance-dependent interactions. The fundamental reason for this is the demanding refresh rate of 500 Hz to 1 kHz which is required due to the sensitivity of the human haptic system.…”

Section: ■ Introductionmentioning

confidence: 99%

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Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

Iakovou

Hayward

Laycock

2017

J. Chem. Inf. Model.

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Haptic technology facilitates user interaction with the virtual world via the sense of touch. In molecular docking, haptics enables the user to sense the interaction forces during the docking process. Here we describe a haptics-assisted interactive software tool, called Haptimol RD, for the study of docking interactions. By utilising GPU-accelerated proximity querying methods very large systems can now be studied.Methods for force scaling, multipoint collision response and haptic navigation are described that address force stability issues that are particular to the interactive docking of large systems. Thus Haptimol RD expands, for the first time, the use of interactive biomolecular haptics to the study of protein-protein interactions. Unlike existing approaches, Haptimol RD is designed to run on relatively inexpensive consumer-level hardware and is freely available to the community.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

Iakovou

Hayward

Laycock

2017

J. Chem. Inf. Model.

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“…They are also useful learning tools for the study of protein-ligand interactions during docking, and research tools for forming and investigating new ideas and hypotheses pertinent to complex formation (e.g. the effects of a mutation) [ 10 ]. Unlike automated approaches, haptics-assisted approaches cannot facilitate the docking of a large number of different protein-ligand targets within a session, due to their interactive nature.…”

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confidence: 99%

Determination of locked interfaces in biomolecular complexes using Haptimol_RD

2016

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Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and gain insights about the docking process itself. Here we use a recently developed haptics software tool, Haptimol_RD, for the rigid docking of protein subunits to form complexes. Dimers, both homo and hetero, are loaded into the software with their subunits separated in space for the purpose of assessing whether they can be brought back into the correct docking pose via rigid-body movements. Four dimers were classified into two types: two with an interwinding subunit interface and two with a non-interwinding subunit interface. It was found that the two with an interwinding interface could not be docked whereas the two with the non-interwinding interface could be. For the two that could be docked a “sucking” effect could be felt on the haptic device when the correct binding pose was approached which is associated with a minimum in the interaction energy. It is clear that for those that could not be docked, the conformation of one or both of the subunits must change upon docking. This leads to the steric-based concept of a locked or non-locked interface. Non-locked interfaces have shapes that allow the subunits to come together or come apart without the necessity of intra-subunit conformational change, whereas locked interfaces require a conformational change within one or both subunits for them to be able to come apart.

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Coarse grained force field for the molecular simulation of natural gases and condensates

Herdes

Totton

Müller

2015

Fluid Phase Equilibria

107

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A c c e p t e d M a n u s c r i p t Highlights -A framework to obtain accurate coarse-grained force fields is described -Force field parameters are presented for compounds of interest -A methodology to simulate bubble points of complex mixtures is proposed. -The force fields are shown to be robust and transferrable Highlights (for review) AbstractThe atomistically-detailed molecular modelling of petroleum fluids is challenging, amongst other aspects, due to the very diverse multicomponent and asymmetric nature of the mixtures in question. Complicating matters further, the time scales for many important processes can be much larger that the current and foreseeable capacity of modern computers running fully-atomistic models. To overcome these limitations, a coarse grained (CG) model is proposed where some of the less-important degrees of freedom are safely integrated out, leaving as key parameters the average energy levels, the molecular conformations and the range of the Mie intermolecular potentials employed as the basis of the model. The parametrization is performed by using an analytical equation of state of the statistical associating fluid theory (SAFT) family to link the potential parameters to macroscopically observed thermophysical properties. The parameters found through this top-down approach are used directly in molecular dynamics simulations of multi-component multi-phase systems. The procedure is exemplified by calculating the phase envelope of the methane-decane binary and of two synthetic light condensate mixtures. A procedure based on a discrete expansion of a mixture is used to determine the bubble points of these latter mixtures, with an excellent agreement to experimental data. The model presented is entirely predictive and an abridged table of parameters for some fluids of interest is provided.

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Computing power revolution and new algorithms: GP-GPUs, clouds and more: general discussion

Cited by 8 publications

References 1 publication

Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

Determination of locked interfaces in biomolecular complexes using Haptimol_RD

Coarse grained force field for the molecular simulation of natural gases and condensates

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