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Paper Abstract and Keywords
Presentation 2026-10-26 13:10
Theoretically and Practically Faster Algorithms for Protein Structure Alignment
Masahito Tsukahara, Tetsuo Shibuya (Tokyo Univ.) COMP2026-12
Abstract (in Japanese) (See Japanese page) 
(in English) Identifying shared substructures in 3D protein models is essential for structural bioinformatics. This task can be modeled as a sequential Largest Common Point-set (LCP) problem under the bottleneck distance.
We propose a new $O(n^{13} log n)$-time exact algorithm for this problem, which improves upon the previous best-known complexity of $O(n^{14})$, where $n$ is the maximum size of the two input structures.
Since these theoretical bounds are practically too large, an $O(n^{7} log n)$-time approximation algorithm with solution-size guarantees has been proposed; however, it remains too time-consuming for practical applications.
Thus, we also propose a new filtering technique to enhance the approximation algorithm without increasing the theoretical time complexity or losing the solution-size guarantees.
Experiments with PDB data show that our technique achieves over a 24-fold speedup at $n=130$.
While the previous algorithm required 3.80 hours on average for $n=130$ in our experiments, making it difficult to test larger structures, our algorithm can process $n=200$ in only 2.33 hours on average.
Our implementation is available at url{https://github.com/masat03110/ProteinStructureAlignmentPlus}.
Keyword (in Japanese) (See Japanese page) 
(in English) structural bioinformatics / pairwise alignment / exact algorithm / approximation algorithm / computational geometry / / /  
Reference Info. IEICE Tech. Rep., vol. 126, no. 210, COMP2026-12, pp. 17-24, Oct. 2026.
Paper # COMP2026-12 
Date of Issue 2026-10-19 (COMP) 
ISSN Online edition: ISSN 2432-6380
Copyright
and
reproduction		 All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034)
Download PDF COMP2026-12

Conference Information
Committee COMP  
Conference Date 2026-10-26 - 2026-10-26 
Place (in Japanese) (See Japanese page) 
Place (in English) 東北大学 川内キャンパス マルチメディア教育研究棟 M601大ホール 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Theoretical Computer Science, etc 
Paper Information
Registration To COMP 
Conference Code 2026-10-COMP 
Language English 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) Theoretically and Practically Faster Algorithms for Protein Structure Alignment 
Sub Title (in English)  
Keyword(1) structural bioinformatics  
Keyword(2) pairwise alignment  
Keyword(3) exact algorithm  
Keyword(4) approximation algorithm  
Keyword(5) computational geometry  
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1st Author's Name Masahito Tsukahara  
1st Author's Affiliation The University of Tokyo (Tokyo Univ.)
2nd Author's Name Tetsuo Shibuya  
2nd Author's Affiliation The University of Tokyo (Tokyo Univ.)
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Speaker Author-1 
Date Time 2026-10-26 13:10:00 
Presentation Time 30 minutes 
Registration for COMP 
Paper # COMP2026-12 
Volume (vol) vol.126 
Number (no) no.210 
Page pp.17-24 
#Pages 8 
Date of Issue 2026-10-19 (COMP) 

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