article

Solving the secondary structure matching problem in cryo-EM de novo modeling using a constrained K-shortest path graph algorithm

Authors:

Mohammad Zubair,

Jing HeAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 11, Issue 2

Pages 419 - 430

https://doi.org/10.1109/TCBB.2014.2302803

Published: 01 March 2014 Publication History

Abstract

Electron cryomicroscopy is becoming a major experimental technique in solving the structures of large molecular assemblies. More and more three-dimensional images have been obtained at the medium resolutions between 5 and 10Å. At this resolution range, major α-helices can be detected as cylindrical sticks and β-sheets can be detected as plain-like regions. A critical question in de novo modeling from cryo-EM images is to determine the match between the detected secondary structures from the image and those on the protein sequence. We formulate this matching problem into a constrained graph problem and present an O(Δ²N²2^N) algorithm to this NP-Hard problem. The algorithm incorporates the dynamic programming approach into a constrained K-shortest path algorithm. Our method, DP-TOSS, has been tested using α-proteins with maximum 33 helices and α-β proteins up to five helices and 12 β-strands. The correct match was ranked within the top 35 for 19 of the 20 α-proteins and all nine α-β proteins tested. The results demonstrate that DP-TOSS improves accuracy, time and memory space in deriving the topologies of the secondary structure elements for proteins with a large number of secondary structures and a complex skeleton.

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Solving the secondary structure matching problem in cryo-EM de novo modeling using a constrained K-shortest path graph algorithm

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Published In

cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 11, Issue 2

March/April 2014

160 pages

ISSN:1545-5963

Editor:
Ying Xu

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IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 March 2014

Accepted: 01 January 2014

Revised: 31 December 2013

Received: 29 July 2013

Published in TCBB Volume 11, Issue 2

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Cited By

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https://dl.acm.org/doi/10.1016/j.compbiolchem.2021.107552
Liu ZCao JTan YXiao QPrasad M(2020)Planning Above the API Clouds Before Flying Above the Clouds: A Real-Time Personalized Air Travel Planning ApproachInternational Journal of Parallel Programming10.1007/s10766-019-00649-848:1(137-156)Online publication date: 1-Feb-2020
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Haslam DZeng TLi RHe JShehu AWu CBoucher CLi JLiu HPop M(2018)Exploratory Studies Detecting Secondary Structures in Medium Resolution 3D Cryo-EM Images Using Deep Convolutional Neural NetworksProceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/3233547.3233704(628-632)Online publication date: 15-Aug-2018
https://dl.acm.org/doi/10.1145/3233547.3233704
Islam TPoteat MHe JHaspel NCowen LShehu AKahveci TPozzi G(2017)Analysis of ß-strand Twist from the 3-dimensional Image of a ProteinProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107507(650-654)Online publication date: 20-Aug-2017
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Al Nasr KYousef FJones CJebril RHaspel NCowen LShehu AKahveci TPozzi G(2017)Geometry Analysis for Protein Secondary Structures Matching ProblemProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107505(716-721)Online publication date: 20-Aug-2017
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Biswas ARanjan DZubair MZeil SNasr KHe J(2017)An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM ImagesIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2016.254372114:3(578-586)Online publication date: 1-May-2017
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Nasr KHe JBaldi PWang W(2014)Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeletonProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2660838(711-716)Online publication date: 20-Sep-2014
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