ArticleProteins2016
Assessment of template-based modeling of protein structure in CASP11.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 34 citations in OpenAlex.
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides.Molecular cancer therapeutics · 2024Review
- Learnable Filters for Geometric Scattering Modules.IEEE transactions on signal processing : a publication of the IEEE Signal Processing Society · 2024Article
- The SGYS motif of TAF15 prion-like domain is critical to amyloid fibril formation.Biophysical journal · 2022Article
- In silico screening, molecular dynamic simulations, and in vitro activity of selected natural compounds as an inhibitor of Leishmania donovani 3-mercaptopyruvate sulfurtransferase.Parasitology research · 2022Article
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment.Proteins · 2021Article
- DATA-DRIVEN LEARNING OF GEOMETRIC SCATTERING MODULES FOR GNNS.IEEE International Workshop on Machine Learning for Signal Processing : [proceedings]. IEEE International Workshop on Machine Learning for Signal Processing · 2021Article
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- A Mutation inJournal of clinical medicine · 2019Article
- Protein Tertiary Structure by Crosslinking/Mass Spectrometry.Trends in biochemical sciences · 2018Review
- Evaluation of the template-based modeling in CASP12.Proteins · 2018Article
- Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.Proteins · 2018Article
- Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.Proteins · 2018Article
- Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies.Proteins · 2017Article
- An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.Acta crystallographica. Section D, Structural biology · 2017Review
- Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?The journal of physical chemistry. B · 2017Article
- Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification.PloS one · 2017Article
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 at 1 institution in 1 country.
Funding
Abstract
We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction). Model quality was judged on the basis of global and local measures of accuracy on all atoms including side chains. The top groups on 39 human-server targets based on model 1 predictions were LEER, Zhang, LEE, MULTICOM, and Zhang-Server. The top groups on 81 targets by server groups based on model 1 predictions were Zhang-Server, nns, BAKER-ROSETTASERVER, QUARK, and myprotein-me. In CASP11, the best models for most targets were equal to or better than the best template available in the Protein Data Bank, even for targets with poor templates. The overall performance in CASP11 is similar to the performance of predictors in CASP10 with slightly better performance on the hardest targets. For most targets, assessment measures exhibited bimodal probability density distributions. Multi-dimensional scaling of an RMSD matrix for each target typically revealed a single cluster with models similar to the target structure, with a mode in the GDT-TS density between 40 and 90, and a wide distribution of models highly divergent from each other and from the experimental structure, with density mode at a GDT-TS value of ∼20. The models in this peak in the density were either compact models with entirely the wrong fold, or highly non-compact models. The results argue for a density-driven approach in future CASP TBM assessments that accounts for the bimodal nature of these distributions instead of Z scores, which assume a unimodal, Gaussian distribution. Proteins 2016; 84(Suppl 1):200-220. © 2016 Wiley Periodicals, Inc.
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.