Protein structure prediction and model quality assessment
By Andriy Kryshtafovych, Krzysztof Fidelis. 2009
115 citations recorded by the source corpus.
Protein structures have proven to be a crucial piece of information for biomedical research. Of the millions of currently sequenced proteins only a small fraction is experimentally solved for structure and the only feasible way to bridge the gap between sequence and structure data is computational modeling. Half a century has passed since it was shown that the amino acid sequence of a protein determines its shape, but a method to translate the sequence code reliably into the 3D structure still remains to be developed. This review summarizes modern protein structure prediction techniques with the emphasis on comparative modeling, and describes the recent advances in methods for theoretical model quality assessment.
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
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- Bohdan Monastyrskyy
- Anna Tramontano
- Yang Zhang
- John Moult
- Liam J. McGuffin
In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- Bohdan Monastyrskyy
- Liam J. McGuffin
- Anna Tramontano
- Yang Zhang
- John Moult
Citations in the corpus
- Critical Assessment of Methods of Protein Structure Prediction (CASP) – Progress and New directions in Round XI (2016, background): “49,58 For example, if a structure model is the basis for interpreting the impact of a genetic mutation, it may be possible to determine whether the local model features are accurate enough for the purpose.”
- Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11 (2015, methodology): “Accuracy estimation methods in CASP11 were evaluated in three subcategories: (1) QAglob: estimation of the global accuracy of models (33 QA groups assessed), where a single score is assigned to a model, (2) QAloc: estimation of the local accuracy of models (21 QA groups assessed), where each residue”
- ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates (2017, background): “However, many biological applications of 3D models are critically dependent on high model accuracy, particularly in key regions, such as binding sites for drug discovery (2).”
- GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function (2015, methodology): “Further, the need to instantiate biologically relevant stereoisomeric forms of individual residues may allow the discrimination of models with native-like versus mirrored topologies using scoring functions for protein model quality assessment at the stage of all-atom reconstruction of the 3D model (”