ArticleScientific reports2013
Protein structure alignment beyond spatial proximity.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- The paraEuropean journal of pain (London, England) · 2026Article
- Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins.Nucleic acids research · 2025Article
- epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.Bioinformatics (Oxford, England) · 2025Article
- Fast, sensitive detection of protein homologs using deep dense retrieval.Nature biotechnology · 2025Article
- PLO3S: Protein LOcal Surficial Similarity Screening.Computational and structural biotechnology journal · 2024Article
- AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.IUBMB life · 2024Article
- Benchmarking reverse docking through AlphaFold2 human proteome.Protein science : a publication of the Protein Society · 2024Article
- Article
- GTalign: spatial index-driven protein structure alignment, superposition, and search.Nature communications · 2024Article
- The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean.The Plant cell · 2024Article
- Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.bioRxiv : the preprint server for biology · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- High-Throughput Screening Method UsingMicroorganisms · 2024Article
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
- Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.Virus evolution · 2024Article
- Dual function of the O-antigen WaaL ligase of Aggregatibacter actinomycetemcomitans.Molecular oral microbiology · 2023Article
- A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.Journal of chemical information and modeling · 2023Article
- Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.Journal of chemical information and modeling · 2023Article
- Structural similarities between the metacyclic and bloodstream form variant surface glycoproteins of the African trypanosome.PLoS neglected tropical diseases · 2023Article
- Origination of LTR Retroelement-Derived NYNRIN Coincides with Therian Placental Emergence.Molecular biology and evolution · 2022Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures.
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