SphereGrinder - reference structure-based tool for quality assessment of protein structural models
By Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, J. Błażewicz. 2015
25 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- David Baker
- Hahnbeom Park
- Sergey Ovchinnikov
- Yang Zhang
- David E. Kim
- Frank DiMaio
- Torsten Schwede
- Andriy Kryshtafovych
In Molecular Biology
- David Baker
- Hahnbeom Park
- Yang Zhang
- Sergey Ovchinnikov
- Torsten Schwede
- Frank DiMaio
- Andriy Kryshtafovych
- David E. Kim
Citations in the corpus
- Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO) (2019, methodology): “To assess the quality of a given protein structure model, numerous scores have been employed such as accuracy of self-estimates (ASE) 18 or cumulative rankings based on various scores such as GDT-TS, 11 lDDT, 9 CAD-score, 8 or Spheregrinder.”
- A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments (2019, methodology): “Compared to the CASP12 web app, the new web app includes (a) distinct coloring of human and server groups in the scores plots (blue indicates at least one model of the cluster was submitted by a server), (c) the possibility to color-code models by residue-wise quality estimates if submitted, and (c)”
- Protein homology model refinement by large-scale energy optimization (2018, methodology): “…simpler and quantitative, we use a single metric — SphereGrinder (SG) (23) — which best captures large-scale structural improvements (3, 8, 11, 22); over the benchmark set the SG values are correlated with both the rmsd and the GDT-HA (global distance test-high accuracy) (24) ( SI Appendix , Fig.”
- Assessment of Refinement of Template-Based Models in CASP11 (2016, methodology): “…native was assessed by comparing their overall backbone conformation using global measures such as RMSD, GDT-TS, and GDT-HA.18 Moreover, the quality of the model was also assessed by using local measures such as LDDT19 and SphereGrinder.20,21 Each of these measures is defined and described below.”