As-Rigid-As-Possible molecular interpolation paths

Nguyen, Minh Khoa; Jaillet, Léonard; Redon, Stéphane

doi:10.1007/s10822-017-0012-y

Cited by 5 publications

(16 citation statements)

References 55 publications

(56 reference statements)

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“…Since its introduction, the development of the ARAP technique has received a lot of attention and led, in particular, to two types of three dimensional (3D) mesh manipulations: interactive modeling through actions on control points and shape interpolation . We have recently proposed the application of the latter for computing molecular interpolation paths . We will now explain the notion of ARAP energy and its application to modeling as used in the ART‐RRT method.…”

Section: Methodsmentioning

confidence: 92%

“…As shown in Ref. [ ], the solution tends to preserve bond lengths and bond angles, and hence, lessen energy variations in molecular structures.…”

Section: Methodsmentioning

confidence: 99%

“…More detailed descriptions of the ComputeCell, ComputeRotation, and ComputePositions functions, also used in the ARAP interpolation process, can be found in Ref. [ ].…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, we propose in this article ART‐RRT, a new method that combines the RRT method with the As‐Rigid‐As‐Possible (ARAP) morphing technique from Computer Graphics to tackle these challenges. The ARAP technique has been successfully applied to find interpolation paths between two conformations of a molecular structure . It has been shown to preserve well the rigidity of the original structures (in particular the bond lengths and bond angles) while allowing large motions during the interpolation.…”

Section: Introductionmentioning

confidence: 99%

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ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

2018

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This article proposes a method to efficiently generate approximate ligand unbinding pathways. It combines an efficient tree-based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is computationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state-of-the-art approaches. We show that the method is time-efficient and produces pathways in good agreement with other state-of-the-art solutions. These paths can serve as first approximations that can be used, analyzed, or improved with more specialized methods. © 2018 Wiley Periodicals, Inc.

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Section: Methodsmentioning

confidence: 92%

“…As shown in Ref. [ ], the solution tends to preserve bond lengths and bond angles, and hence, lessen energy variations in molecular structures.…”

Section: Methodsmentioning

confidence: 99%

“…More detailed descriptions of the ComputeCell, ComputeRotation, and ComputePositions functions, also used in the ARAP interpolation process, can be found in Ref. [ ].…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

2018

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“…The As-Rigid-As-Possible(ARAP) approach (Nguyen, et al, 2017) applies mesh distortion techniques used in computer graphics. A topology is created based…”

mentioning

confidence: 99%

Morphing and docking visualisation of biomolecular structures using Multi-Dimensional Scaling

Veevers

Hayward

2018

Journal of Molecular Graphics and Modelling

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Protein structures are often solved at atomic resolution in two states defining a functional movement but intervening conformations are usually unknown. Morphing methods generate intervening conformations between two known structures. When viewed as an animation using molecular graphics, a smooth, direct morph enables the eye to track changes in structure that might be otherwise missed. We present a morphing method that aims to linearly interpolate interatomic distances and which uses SMACOF (Scaling by MAjorisation of COmplicated Function) and multigrid techniques with a cut-off distance based weighting that optimizes the MolProbity score of intervening structures. The all-atom morphs are smooth, move directly between the two structures, and are shown, in general, to pass closer to a set of known intermediates than those generated using other methods. The techniques are also used for docking by putting the unbound structures in a "near-approach pose" and then morphing to the bound complex. The resulting GPU-accelerated tools are available on a webserver, Morphit_Pro, at http://morphit-pro.cmp.uea.ac.uk/ and more than 5000 domains movements available at the DynDom website can now be viewed as morphs http://morphit-pro.cmp.uea.ac.uk/dyndom/.

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Generating conformational transition paths with low potential-energy barriers for proteins

Nguyen

Jaillet

Redon

2018

J Comput Aided Mol Des

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The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.

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As-Rigid-As-Possible molecular interpolation paths

Cited by 5 publications

References 55 publications

ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

Morphing and docking visualisation of biomolecular structures using Multi-Dimensional Scaling

Generating conformational transition paths with low potential-energy barriers for proteins

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