An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data.

Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu

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Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Detection of circular permutations by Protein Language Models.Computational and structural biotechnology journal · 2025
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Authors and funding

4 authors.

Jianbo LuHuman Genetics Resource Center, National Research Institute for Family Planning, Beijing, 100081 China ; Graduate School of Peking Union Medical College, Beijing, 100730 China.

Guoliang XuNational Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China.

Shihua ZhangNational Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China.

Benzhuo LuNational Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSuperpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address the missing data crudely by ignoring such atoms from their structures.

resultsIn this paper, we propose an effective method for superpositioning pairwise and multiple structures without sequence alignment. It is a two-stage procedure including data reduction and data registration.

conclusionsNumerical experiments demonstrated that our method is effective and efficient. The code package of protein structure superposition method for addressing the cases with missing data is implemented by MATLAB, and it is freely available from: http://sourceforge.net/projects/pssm123/files/?source=navbar.

Indexed as

Iterative closest pointProtein structure alignmentSuperposition

Identifiers

PMID27330544

DOI10.1186/s13015-016-0079-3

PMCPMC4915111

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