ArticleProteins2018
Assessment of the model refinement category in CASP12.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences.Protein science : a publication of the Protein Society · 2022Article
- Article
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment.Proteins · 2021Article
- Evaluation of model refinement in CASP14.Proteins · 2021Article
- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy.International journal of molecular sciences · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Probabilistic divergence of a template-based modelling methodology from the ideal protocol.Journal of molecular modeling · 2021Article
- Conservation of binding properties in protein models.Computational and structural biotechnology journal · 2021Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- Article
- High-accuracy refinement using Rosetta in CASP13.Proteins · 2019Article
- Evaluation of model refinement in CASP13.Proteins · 2019Article
- GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure.Nucleic acids research · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Forging tools for refining predicted protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Void distributions reveal structural link between jammed packings and protein cores.Physical review. E · 2019Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.Protein science : a publication of the Protein Society · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the previous experiments, the predictors were invited to refine selected server models received in the regular (nonrefinement) stage of the CASP experiment. We assessed the submitted models using a combination of standard CASP measures. The coefficients for the linear combination of Z-scores (the CASP12 score) have been obtained by a machine learning algorithm trained on the results of visual inspection. We identified eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Albeit the top methods adopted distinctively different approaches, their overall performance was almost indistinguishable, with each of them excelling in different scores or target subsets. What is more, there were a few novel approaches that, while doing worse than average in most cases, provided the best refinements for a few targets, showing significant latitude for further innovation in the field.
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.