RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules

Neveu, Émilie; Popov, Petr; Hoffmann, Alexandre; Migliosi, Angelo; Besseron, Xavier; Danoy, Grégoire; Bouvry, Pascal; Grudinin, Sergei

doi:10.1093/bioinformatics/bty160

Cited by 21 publications

(16 citation statements)

References 57 publications

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“…Inspired by the quaternion arithmetic applied to the best superposition of a set of points [21,22,23] together with our recent developments [24,25], we propose a new symmetry measure and an analytical method to find the best symmetry axes of a symmetrical assembly possessing a cyclic C n symmetry. We should specifically emphasize that our method assumes that the pointto-point correspondence between the different subunits of the assembly is known.…”

Section: Introductionmentioning

confidence: 99%

Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Pagès

Kinzina

Grudinin

2018

Journal of Structural Biology

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Symmetry in protein, and, more generally, in macromolecular assemblies is a key point to understand their structure, stability and function. Many symmetrical assemblies are currently present in the Protein Data Bank (PDB) and some of them are among the largest solved structures, thus an efficient computational method is needed for the exhaustive analysis of these. The cyclic symmetry groups represent the most common assemblies in the PDB. These are also the building blocks for higher-order symmetries. This paper presents a mathematical formulation to find the position and the orientation of the symmetry axis in a cyclic symmetrical protein assembly, and also to assess the quality of this symmetry. Our method can also detect symmetries in partial assemblies. We provide an efficient C++ implementation of the method and demonstrate its efficiency on several examples including partial assemblies and pseudo symmetries. We also compare the method with two other published techniques and show that it is significantly faster on all the tested examples. Our method produces results with a machine precision, its cost function is solely based on 3D Euclidean geometry, and most of the operations are performed analytically. The method is available athttp://team.inria.fr/nano-d/software/ananas. The graphical user interface of the method built for the SAMSON platform is available athttp://samson-connect.net.

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Section: Introductionmentioning

confidence: 99%

Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Pagès

Kinzina

Grudinin

2018

Journal of Structural Biology

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“…However, in general case, the complexity of the RMSD computation is linear with respect to the number of atoms in a molecule. Nonetheless, recently, we showed that in a particular case of orthogonal deformations, it is possible to compute RMSD much faster . Thus, it will be interesting to extend Carbon as the flexible refinement method using the orthogonal deformations, such as normal modes, in the further studies.…”

Section: Discussionmentioning

confidence: 99%

Controlled‐advancement rigid‐body optimization of nanosystems

et al. 2019

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In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertiaweighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein-protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net.

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“…As an alternative to lRMSD calculations based on matrix decompositions-such as SVD, a fast determination of the optimal rotation matrix based on a Newton-Raphson quaternion-based method was reported [4]. Finally, recent work addressed the calculation of RMSD between flexible structures, the flexibility being modeled using collective coordinates obtained via normal mode analysis or PCA [15]. This latter work is especially interesting as it targets deformable structures modeled by means of collective motions.…”

Section: Rmsd Lrmsd and Their Variantsmentioning

confidence: 99%

Characterizing molecular flexibility by combining lRMSD measures

Cazals

Tetley

2018

Preprint

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The root mean square deviation (RMSD) and the least RMSD are two widely used similarity measures in structural bioinformatics. Yet, they stem from global comparisons, possibly obliterating locally conserved motifs. We correct these limitations with the so-called combined RMSD , which mixes independent lRMSD measures, each computed with its own rigid motion. The combined RMSD can be used to compare (quaternary) structures based on motifs defined from the sequence (domains, SSE), or to compare structures based on structural motifs yielded by local structural alignment methods.We illustrate the benefits of combined RMSD over the usual RMSD on three problems, namely (i) the analysis of conformational changes based on combined RMSD of rigid structural motifs (case study: a class II fusion protein), (ii) the calculation of structural phylogenies (case study: class II fusion proteins), and (iii) the assignment of quaternary structures for hemoglobin. Using these, we argue that the combined RMSD is a tool a choice to perform positive and negative discrimination of degree of freedom, with applications to the design of move sets and collective coordinates.Combined RMSD are available within the Structural Bioinformatics Library (http://sbl.inria.fr).

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RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 21 publications

References 57 publications

Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Analytical symmetry detection in protein assemblies. I. Cyclic symmetries

Controlled‐advancement rigid‐body optimization of nanosystems

Characterizing molecular flexibility by combining lRMSD measures

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