ArticleActa crystallographica. Section D, Biological crystallography2012
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 404 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
404 citing papers in PubMed.
- Trial
- Article
- Generative design of programmable asymmetric β-barrel nanopores.bioRxiv : the preprint server for biology · 2026Article
- Improved hydrolysis of piperacillin by OXA-48-like R214G variants, a selective advantage under piperacillin-tazobactam exposure.Antimicrobial agents and chemotherapy · 2026Article
- Structural basis of porcine reproductive and respiratory syndrome virus 2 neutralization by a GP4-targeting monoclonal antibody.The Journal of general virology · 2026Article
- Fragment-Based Design of Targeted Covalent Inhibitors: The Scope and Limitation of Linking Approaches.ChemMedChem · 2026Article
- Monoclonal antibodies against nitrated nerve growth factor reveal an oxidation-dependent pathogenic hallmark in ALS.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Structural ontogeny of protein-protein interactions.Science (New York, N.Y.) · 2026Article
- Ligand non-competitive GITR antibody prevents formation of the obligatory signal-triggering GITRL: GITR stoichiometry.Scientific reports · 2025Article
- Hyperagonism of a Vitamin D Receptor Agonist/Histone Deacetylase Inhibitor Hybrid Molecule.Journal of medicinal chemistry · 2025Article
- Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors.Nature communications · 2025Article
- Article
- High-throughput crystallographic fragment screening of Zika virus NS3 Helicase.bioRxiv : the preprint server for biology · 2025Article
- Modulating the Binding Kinetics of Bruton's Tyrosine Kinase Inhibitors through Transition-State Effects.Journal of the American Chemical Society · 2025Article
- Derivatives of MOPS: promising scaffolds for SARS coronaviruses Macro domain-targeted inhibition.The FEBS journal · 2025Article
- Chemical Evolution of Early Macromolecules: From Prebiotic Oligopeptides to Self-Organizing Biosystems via Amyloid Formation.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- NI-3201 Is a Bispecific Antibody Mediating PD-L1-Dependent CD28 Co-stimulation on T Cells for Enhanced Tumor Control.Cancer immunology research · 2025Article
- Broadly neutralizing antibodies isolated from HEV convalescents confer protective effects in human liver-chimeric mice.Nature communications · 2025Article
- Mechanisms of neutralization of toxSAS from toxin-antitoxin modules.Nature chemical biology · 2025Article
344 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct 'target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.