ArticleBMC bioinformatics2011
A novel method to compare protein structures using local descriptors.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Graph neural network and diffusion model for modeling RNA interatomic interactions.Bioinformatics (Oxford, England) · 2025Article
- ICARUS: flexible protein structural alignment based on Protein Units.Bioinformatics (Oxford, England) · 2023Article
- Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations.Frontiers in molecular biosciences · 2021Article
- Article
- Structural alignment of protein descriptors - a combinatorial model.BMC bioinformatics · 2016Article
- WeBIAS: a web server for publishing bioinformatics applications.BMC research notes · 2015Article
- Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.Journal of molecular modeling · 2014Article
- MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.BMC bioinformatics · 2013Article
- Binding Stoichiometry of a Recombinant Selenophosphate Synthetase with One Synonymic Substitution E197D to a Fluorescent Nucleotide Analog of ATP, TNP-ATP.Journal of amino acids · 2013Article
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2 authors.
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Abstract
backgroundProtein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships.
resultsWe present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL). Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method's capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77% (the second best method tested achieves 60% accuracy).
conclusionsDEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL.
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