Deformation Invariant Local Descriptors for Protein Surface Comparison

Abstract Motivation Global protein surface comparison (GPSC) studies have been limited compared to other research works on protein structure alignment/comparison due to lack of real applications associated with GPSC. However, the technology advances in cryo-electron tomography (CET) have made methods to identify proteins from their surface shapes extremely useful. Results In this study, we developed a new method called Farthest point sampling (FPS)-enhanced Triangulation-based Iterative-closest-Point (ICP) (FTIP) for GPSC. We applied it to protein classification using only surface shape information. Our method first extracts a set of feature points from protein surfaces using FPS and then uses a triangulation-based efficient ICP algorithm to align the feature points of the two proteins to be compared. Tested on a benchmark dataset with 2329 proteins using nearest-neighbor classification, FTIP outperformed the state-of-the-art method for GPSC based on 3D Zernike descriptors. Using real and simulated cryo-EM data, we show that FTIP could be applied in the future to address problems in protein identification in CET experiments. Availability and implementation Programs/scripts we developed/used in the study are available at http://ani.stat.fsu.edu/∼yuan/index.fld/FTIP.tar.bz2. Supplementary information Supplementary data are available at Bioinformatics online.

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FTIP - An Accurate and Efficient Method for Global Protein Surface Comparison

Biophysical Journal ◽

10.1016/j.bpj.2019.11.2766 ◽

2020 ◽

Vol 118 (3) ◽

pp. 501a

Author(s):

Yuan Zhang ◽

Xin Sui ◽

Scott M. Stagg ◽

Jinfeng Zhang

Keyword(s):

Efficient Method ◽

Protein Surface ◽

Surface Comparison

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3D-SURFER: software for high-throughput protein surface comparison and analysis

Bioinformatics ◽

10.1093/bioinformatics/btp542 ◽

2009 ◽

Vol 25 (21) ◽

pp. 2843-2844 ◽

Cited By ~ 46

Author(s):

David La ◽

Juan Esquivel-Rodríguez ◽

Vishwesh Venkatraman ◽

Bin Li ◽

Lee Sael ◽

...

Keyword(s):

High Throughput ◽

Protein Surface ◽

Comparison And Analysis ◽

Surfer Software ◽

Surface Comparison

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Improved protein surface comparison and application to low-resolution protein structure data

BMC Bioinformatics ◽

10.1186/1471-2105-11-s11-s2 ◽

2010 ◽

Vol 11 (S11) ◽

Cited By ~ 14

Author(s):

Lee Sael ◽

Daisuke Kihara

Keyword(s):

Protein Structure ◽

Structure Data ◽

Low Resolution ◽

Protein Surface ◽

Protein Structure Data ◽

Surface Comparison

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Modelling of the trajectories of particles conveyed by a gaseous jet onto a plane surface. Comparison with experience

International Journal of Multiphase Flow ◽

10.1016/s0301-9322(97)88531-x ◽

1996 ◽

Vol 22 ◽

pp. 142

Author(s):

J Lede

Keyword(s):

Plane Surface ◽

Surface Comparison

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Gymnomitrion fissum (Gymnomitriaceae, Marchantiophyta) — a new species with fissured leaf surface from China

Novosti sistematiki nizshikh rastenii ◽

10.31111/nsnr/2017.51.274 ◽

2017 ◽

Vol 51 ◽

pp. 274-280

Author(s):

A. D. Potemkin ◽

Yu. S. Mamontov ◽

N. S. Gamova

Keyword(s):

New Species ◽

Cross Sections ◽

Cell Walls ◽

Leaf Surface ◽

Outer Cell ◽

Sem Images ◽

Cell Lumen ◽

A New Species ◽

Surface Comparison

Study of selected specimens of Gymnomitrion collected by D. G. Long in Yunnan, China, revealed a new species, G. fissum Mamontov et Potemkin, sp. nov., with a fissured leaf surface. Comparison of SEM images of the leaf surface and leaf cross sections shows that the leaf surface of G. fissum is different from that of other known species with a superficially similar leaf surface, i. e. Mylia taylorii, M. verrucosa s. l. and Trabacellula tumidula. It has fissures around the cell lumen rather than grids and perforations. Outer cell walls of Gymnomitrion fissum are much thicker than in Mylia taylorii, M. verrucosa s. l. and Trabacellula tumidula, and their outer layers tend to be partly or completely caducous. G. fissum is related to the group of species assigned to the former genus Apomarsupella.

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