ArticleeLife2012
Modelling dynamics in protein crystal structures by ensemble refinement.
Article in eLife, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 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
188 citing papers in PubMed.
- Multistate Enzyme Design Enables Efficient and Stereoselective Multistep Catalysis.bioRxiv : the preprint server for biology · 2026Article
- Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors.Biophysical journal · 2026Article
- Intracellular pocket and ICL2 motifs govern G-protein coupling bias in NKThe Journal of biological chemistry · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.Nature chemical biology · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- Statistical crystallography reveals an allosteric network in SARS-CoV-2 MCommunications biology · 2026Article
- Structural basis of chaperone mechanisms in cells and the evolutionary emergence of the protein world.bioRxiv : the preprint server for biology · 2026Article
- Article
- The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026Article
- Comparing Multislice Projections of MD Simulations with CryoEM Exposes Structural Prediction Errors.bioRxiv : the preprint server for biology · 2026Article
- Unfreezing structural biology for drug discovery.Nature chemical biology · 2026Review
- Dynamical network analysis reveals long-range residue couplings at the pMHC interface underlying enhanced immunogenicity.NPJ systems biology and applications · 2026Article
- Structural characterization of metal binding in human tyrosylprotein sulfotransferase 2, TPST2.Scientific reports · 2026Article
- Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A proteome-wide biochemical screen defines binding determinants of the core autophagy protein LC3B.bioRxiv : the preprint server for biology · 2026Article
- Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling.bioRxiv : the preprint server for biology · 2025Article
- Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.bioRxiv : the preprint server for biology · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- The initial dynamics of product release in terpene synthases-The case of CotB2.Protein science : a publication of the Protein Society · 2025Article
128 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
4 authors.
Funding
Abstract
Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation-libration-screw (TLS) model. Modeling of 20 protein datasets at 1.1-3.1 Å resolution reduced cross-validated R(free) values by 0.3-4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a 'molten core' likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order-disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure-dynamics-function relationships.DOI:http://dx.doi.org/10.7554/eLife.00311.001.
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.