ArticleInternational journal of molecular sciences2019
Towards Unraveling the Histone Code by Fragment Blind Docking.
Article in International journal of molecular sciences, 2019. 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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Who cites it
9 citing papers in PubMed.
- Swarm Intelligence in Drug Discovery Applications: Unlocking Deeper Insights on the Identification and Optimization of Potential Drug Candidates.Drug design, development and therapy · 2026Review
- The Redesign of the Molecular Scaffold of Viral Ion Channel Blockers.Computational and structural biotechnology journal · 2026Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Construction of Histone-Protein Complex Structures by Peptide Growing.International journal of molecular sciences · 2023Article
- Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4.International journal of molecular sciences · 2022Article
- Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Determination of Ligand Binding Modes in Hydrated Viral Ion Channels to Foster Drug Design and Repositioning.Journal of chemical information and modeling · 2021Article
- Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome.International journal of molecular sciences · 2020Review
- Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Histones serve as protein spools for winding the DNA in the nucleosome. High variability of their post-translational modifications result in a unique code system often responsible for the pathomechanisms of epigenetics-based diseases. Decoding is performed by reader proteins via complex formation with the N-terminal peptide tails of histones. Determination of structures of histone-reader complexes would be a key to unravel the histone code and the design of new drugs. However, the large number of possible histone complex variations imposes a true challenge for experimental structure determination techniques. Calculation of such complexes is difficult due to considerable size and flexibility of peptides and the shallow binding surfaces of the readers. Moreover, location of the binding sites is often unknown, which requires a blind docking search over the entire surface of the target protein. To accelerate the work in this field, a new approach is presented for prediction of the structure of histone H3 peptide tails docked to their targets. Using a fragmenting protocol and a systematic blind docking method, a collection of well-positioned fragments of the H3 peptide is produced. After linking the fragments, reconstitution of anchoring regions of the target-bound H3 peptide conformations was possible. As a first attempt of combination of blind and fragment docking approaches, our new method is named fragment blind docking (FBD).
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