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Similarity Search of Flexible 3D Molecules Combining Local and Global Shape Descriptors

Authors:

Apostolos Axenopoulos,

Dimitrios Rafailidis,

Georgios Papadopoulos,

Elias N. Houstis,

Petros DarasAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 13, Issue 5

Pages 954 - 970

https://doi.org/10.1109/TCBB.2015.2498553

Published: 01 September 2016 Publication History

Abstract

In this paper, a framework for shape-based similarity search of 3D molecular structures is presented. The proposed framework exploits simultaneously the discriminative capabilities of a global, a local, and a hybrid local-global shape feature to produce a geometric descriptor that achieves higher retrieval accuracy than each feature does separately. Global and hybrid features are extracted using pairwise computations of diffusion distances between the points of the molecular surface, while the local feature is based on accumulating pairwise relations among oriented surface points into local histograms. The local features are integrated into a global descriptor vector using the bag-of-features approach. Due to the intrinsic property of its constituting shape features to be invariant to articulations of the 3D objects, the framework is appropriate for similarity search of flexible 3D molecules, while at the same time it is also accurate in retrieving rigid 3D molecules. The proposed framework is evaluated in flexible and rigid shape matching of 3D protein structures as well as in shape-based virtual screening of large ligand databases with quite promising results.

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Cited By

Puertas-Martín SRedondo JBanegas-Luna AGarzón EPérez-Sánchez HGillet VOrtigosa P(2022)Virtual Screening Based on Electrostatic Similarity and Flexible LigandsComputational Science and Its Applications – ICCSA 2022 Workshops10.1007/978-3-031-10562-3_10(127-139)Online publication date: 4-Jul-2022
https://dl.acm.org/doi/10.1007/978-3-031-10562-3_10
Puertas-Martín SRedondo JGarzón EPérez-Sánchez HOrtigosa P(2022)Increasing the Accuracy of Optipharm’s Virtual Screening Predictions by Implementing Molecular FlexibilityBioinformatics and Biomedical Engineering10.1007/978-3-031-07802-6_20(234-245)Online publication date: 27-Jun-2022
https://dl.acm.org/doi/10.1007/978-3-031-07802-6_20
Zhang DWu ZWang XLv CZhou M(2021)3D non-rigid shape similarity measure based on Fréchet distance between spectral distance distribution curveMultimedia Tools and Applications10.1007/s11042-020-09420-580:1(615-640)Online publication date: 1-Jan-2021
https://dl.acm.org/doi/10.1007/s11042-020-09420-5
Show More Cited By

Similarity Search of Flexible 3D Molecules Combining Local and Global Shape Descriptors
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Machine learning
    1. Learning paradigms
      1. Unsupervised learning

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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 13, Issue 5

September 2016

193 pages

ISSN:1545-5963

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IEEE Computer Society Press

Washington, DC, United States

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Published: 01 September 2016

Published in TCBB Volume 13, Issue 5

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Cited By

Puertas-Martín SRedondo JBanegas-Luna AGarzón EPérez-Sánchez HGillet VOrtigosa P(2022)Virtual Screening Based on Electrostatic Similarity and Flexible LigandsComputational Science and Its Applications – ICCSA 2022 Workshops10.1007/978-3-031-10562-3_10(127-139)Online publication date: 4-Jul-2022
https://dl.acm.org/doi/10.1007/978-3-031-10562-3_10
Puertas-Martín SRedondo JGarzón EPérez-Sánchez HOrtigosa P(2022)Increasing the Accuracy of Optipharm’s Virtual Screening Predictions by Implementing Molecular FlexibilityBioinformatics and Biomedical Engineering10.1007/978-3-031-07802-6_20(234-245)Online publication date: 27-Jun-2022
https://dl.acm.org/doi/10.1007/978-3-031-07802-6_20
Zhang DWu ZWang XLv CZhou M(2021)3D non-rigid shape similarity measure based on Fréchet distance between spectral distance distribution curveMultimedia Tools and Applications10.1007/s11042-020-09420-580:1(615-640)Online publication date: 1-Jan-2021
https://dl.acm.org/doi/10.1007/s11042-020-09420-5
Zhao ZLi BLiu J(2021)Fitting PB1-p62 filaments model structure into its electron microscopy based on an improved genetic algorithmJournal of Combinatorial Optimization10.1007/s10878-019-00483-142:4(937-947)Online publication date: 1-Nov-2021
https://dl.acm.org/doi/10.1007/s10878-019-00483-1
Langenfeld FAxenopoulos AChatzitofis ACraciun DDaras PDu BGiachetti ALai YLi HLi YMasoumi MPeng YRosin PSirugue JSun LThermos SToews MWei YWu YZhai YZhao TZheng YMontes MVeltkamp RTelea ATheoharis T(2018)Protein shape retrievalProceedings of the 11th Eurographics Workshop on 3D Object Retrieval10.5555/3290638.3290648(53-61)Online publication date: 16-Apr-2018
https://dl.acm.org/doi/10.5555/3290638.3290648

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