ArticleProtein science : a publication of the Protein Society2012
Protein structure validation by generalized linear model root-mean-square deviation prediction.
Article in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer.BMC pharmacology & toxicology · 2021Article
- Computational Design and Preliminary Serological Analysis of a Novel Multi-Epitope Vaccine Candidate against Onchocerciasis and Related Filarial Diseases.Pathogens (Basel, Switzerland) · 2021Article
- Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication.The Journal of biological chemistry · 2019Article
- De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.Nature chemistry · 2017Article
- Robust and transferable quantification of NMR spectral quality using IROC analysis.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2017Article
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- Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development.Journal of molecular modeling · 2016Article
- DockTope: a Web-based tool for automated pMHC-I modelling.Scientific reports · 2015Article
- The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.Journal of biomolecular NMR · 2015Article
- Structural determinants of the interaction between the TpsA and TpsB proteins in the Haemophilus influenzae HMW1 two-partner secretion system.Journal of bacteriology · 2015Article
- An overview of tools for the validation of protein NMR structures.Journal of biomolecular NMR · 2014Review
- Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.Journal of chemical information and modeling · 2014Article
- Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.Journal of the American Chemical Society · 2014Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
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5 authors.
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Abstract
Large-scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD-NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root-mean-square deviation (RMSD) value between the present structure and the (unavailable) "true" structure (GLM-RMSD). For two sets of structural models from the CASD-NMR and CASP projects, this GLM-RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. "true") heavy-atom RMSDs were 0.69 and 0.76, for the two datasets from CASD-NMR and CASP, respectively, which is considerably higher than those for the individual scores (-0.24 to 0.68). The GLM-RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate-based quality scores.
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