ArticleProteins2022
Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.
Article in Proteins, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Dockground: Expanding the Resource to Protein-DNA Complexes.Journal of molecular biology · 2026Article
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.Proteins · 2022Article
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Authors and funding
2 authors.
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Abstract
We explored the Protein Data Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.
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