ArticleActa crystallographica. Section D, Structural biology2021
New restraints and validation approaches for nucleic acid structures in PDB-REDO.
Article in Acta crystallographica. Section D, Structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Reconstructing biological molecules with help from video gamers.Acta crystallographica. Section D, Structural biology · 2025Article
- AQuaRef: machine learning accelerated quantum refinement of protein structures.Nature communications · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- Centrosome‑, mitotic spindle‑ and cytokinetic bridge‑specific compartmentalization of AGO2 protein in human liver cells undergoing mitosis: Non‑canonical, RNAi‑dependent, control of local homeostasis.Molecular medicine reports · 2025Article
- The adaptability of the fungal tRNA ligase's ATP-binding pocket: a potential target for new antifungal drugs.NAR molecular medicine · 2025Article
- Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins.Scientific reports · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Article
- The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans.Nature communications · 2024Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.International journal of biological macromolecules · 2022Article
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Authors and funding
8 authors.
Funding
Abstract
The quality of macromolecular structure models crucially depends on refinement and validation targets, which optimally describe the expected chemistry. Commonly used software for these two procedures has been designed and developed in a protein-centric manner, resulting in relatively few established features for the refinement and validation of nucleic acid-containing structure models. Here, new nucleic acid-specific approaches implemented in PDB-REDO are described, including a new restraint model using noncovalent geometries (base-pair hydrogen bonding and base-pair stacking) as refinement targets. New validation routines are also presented, including a metric for Watson-Crick base-pair geometry normality (Z
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