Evaluating the usefulness of protein structure models for molecular replacement

By Alejandro Giorgetti, Domenico Raimondo, Adriana Erica Miele, Anna Tramontano. 2005

65 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, background): “The correspondence between the GDT_TS and the difﬁculty of MR has been noted previously (Giorgetti et al., 2005).”
Replacement (1980, methodology): “Other developments include Auto-Rickshaw (Panjikar et al. , 2005), which is principally for experimental phasing but covers phased MR as well, and a scheme for using comparative models in MR (Giorgetti et al. , 2005).”
Automated search-model discovery and preparation for structure solution by molecular replacement. (2007, methodology): “Other developments include Auto-Rickshaw (Panjikar et al., 2005), which is principally for experimental phasing but covers phased MR as well, Balbes (Long et al., 2007) and a scheme for using comparative models in MR (Giorgetti et al., 2005).”
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “Anna Tramontano and coworkers tested the utility of theoretical models submitted to the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment.”
GOMoDo: A GPCRs Online Modeling and Docking Webserver (2013, background): “Nonetheless, homology modeling has succeeded in predicting ligand-target interactions information for several different GPCRs [3–6].”
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “Previously, a GDT-TS score of >0.8 was thought to be required for successful MR (Giorgetti et al., 2005).”
Protein Structure Prediction: Is It Useful? (2009, methodology): “As another application of homologous modeling, Tramontano and co-workers [13 ] evaluated the usefulness of models predicted in CASP experiments for molecular replacement (MR), a procedure for recovering the phase information in X-ray diffraction studies, which is crucial for determining the electron”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “…biological applications (9–11), such as rational design of mutagenesis experiments (12), providing receptor models for virtual screening (13, 14), to develop strategies for protein engineering, or to support experimental structure solution by crystallography (15, 16) or electron microscopy (17–19).”
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, background): “al (Giorgetti et al., 2005) demonstrated that the Global Distance Test Mao et al.”
High resolution protein structure prediction and the crystallographic phase problem (2007, methodology): “metrics for comparing models with crystal structures; (5) screening of models”
Assessment of protein structure refinement in CASP9 (2011, methodology): “35–38 We estimate the quality of the predictions for this purpose by calculating the z -score of the best orientation of the model in the unit cell of the crystal with respect to placing it in a set of random orientations (for more details see Supporting Information and Ref.”