Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design

Rossi, Romain; Isorce, Mathieu; Morin, Sandy; Flocard, Julien; Arumugam, Karthik; Crouzy, Serge; Vivaudou, Michel; Redon, Stéphane

doi:10.1093/bioinformatics/btm191

Cited by 30 publications

(39 citation statements)

References 15 publications

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“…Finally we want to determine whether the cartesian adaptive approach may be combined with an adaptive internal degrees-of-freedom simulation method [18], i.e. group atoms into clusters which might deform while creating and breaking bonds, which should provide great functionality both for simulation and digital prototyping.…”

Section: Resultsmentioning

confidence: 99%

“…In this case, the two-body potential expression can be introduced efficiently in our adaptive approach thanks to the notion of partial forces. [18] As illustrated in Figure 4, the preferred orientation of the fullerene is always with a six-membered ring parallel to the surface. The agreement with other calculations and experiments is very satisfactory.…”

Section: Extension Of the Brenner Potentialmentioning

confidence: 97%

“…[18] As a result, we assume in this paper that, when we need to update forces and energies at each time step, we are given the list of pairs of neighboring atoms whose relative position has changed due to user actions or to adaptive minimization.…”

Section: Interactive Physically-based Structural Modelingmentioning

confidence: 99%

“…[18] The method relies on partial updates of neighbor lists and interaction potentials and forces, which are made possible by incremental updates of the molecular state description (precisely, only a subset of the torsional degrees of freedom are moved at each time step). The other key feature is an efficient algorithm able to predict which degrees of freedom are the most important.…”

Section: Introductionmentioning

confidence: 99%

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Interactive physically-based structural modeling of hydrocarbon systems

Bosson

Grudinin

Bouju

et al. 2012

Journal of Computational Physics

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Hydrocarbon systems have been intensively studied via numerical methods, including electronic structure computations, molecular dynamics and Monte Carlo simulations. Typically, these methods require an initial structural model (atomic positions and types, topology, etc.) that may be produced using scripts and/or modeling tools. For many systems, however, these building methods may be ineffective, as the user may have to specify the positions of numerous atoms while maintaining structural plausibility.In this paper, we present an interactive physically-based modeling tool to construct structural models of hydrocarbon systems. As the user edits the geometry of the system, atomic positions are also influenced by the Brenner potential, a well-known bond-order reactive potential. In order to be able to interactively edit systems containing numerous atoms, we introduce a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated is decoupled from the number of atoms in the system. We show that our approach may be used to effectively build realistic models of hydrocarbon structures that would be difficult or impossible to produce using other tools.

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Section: Resultsmentioning

confidence: 99%

Section: Extension Of the Brenner Potentialmentioning

confidence: 97%

Section: Interactive Physically-based Structural Modelingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Interactive physically-based structural modeling of hydrocarbon systems

Bosson

Grudinin

Bouju

et al. 2012

Journal of Computational Physics

Self Cite

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“…This is avoided in an ENM, although it is known that some key aspects of dynamical behaviour of biomolecules at physiological temperature are not well described by the harmonic model. Bolopion et al [23] have recently developed a tool that allows the user to interact with a molecular simulation based on quasi-statics [24], via a haptic feedback device. They give details on the coupling between the haptic device and the molecular simulation.…”

Section: Introductionmentioning

confidence: 99%

Applying forces to elastic network models of large biomolecules using a haptic feedback device

Stocks

Laycock

Hayward

2011

J Comput Aided Mol Des

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Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.

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Interactive Chemical Reactivity Exploration

et al. 2014

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Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transitionstate structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.

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Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design

Cited by 30 publications

References 15 publications

Interactive physically-based structural modeling of hydrocarbon systems

Interactive physically-based structural modeling of hydrocarbon systems

Applying forces to elastic network models of large biomolecules using a haptic feedback device

Interactive Chemical Reactivity Exploration

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