ArticleJournal of chemical theory and computation2012
FlexE: Using elastic network models to compare models of protein structure.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Which Metrics Best Capture Protein Structural Changes in Molecular Dynamics Simulations? Evaluating Score Combinations and Force-Field Effects.Journal of chemical information and modeling · 2026Article
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Evaluation of model refinement in CASP14.Proteins · 2021Article
- Quantifying steric hindrance and topological obstruction to protein structure superposition.Algorithms for molecular biology : AMB · 2021Article
- Blind protein structure prediction using accelerated free-energy simulations.Science advances · 2016Article
- Article
- Ensemble-based evaluation for protein structure models.Bioinformatics (Oxford, England) · 2016Article
- Article
- On the importance of the distance measures used to train and test knowledge-based potentials for proteins.PloS one · 2014Article
- lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.Bioinformatics (Oxford, England) · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
It is often valuable to compare protein structures to determine how similar they are. Structure comparison methods such as RMSD and GDT-TS are based solely on fixed geometry and do not take into account the intrinsic flexibility or energy landscape of the protein. We propose a method, which we call FlexE, that is based on a simple elastic network model and uses the deformation energy as measure of the similarity between two structures. FlexE can distinguish biologically relevant conformational changes from random changes, while existing geometry-based methods cannot. Additionally, FlexE incorporates the concept of thermal energy, which provides a rational way to determine when two models are "the same". FlexE provides a unique measure of the similarity between protein structures that is complementary to existing methods.
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.