LGA: a method for finding 3D similarities in protein structures

By Adam T. Zemla. 2003

1,102 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, 3D Vision & Pose, Computational Biology & Bioinformatics

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Citations in the corpus

Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “…31 which was used to compute TM-score through a heuristic alignment approach improving on the original RNA-align 29 ; (2) Local – Global Alignment 32 which yielded GDT_TS, the average percentage of aligned C4 0 atoms (rather than that of C α in proteins) at cutoffs of 1 Å, 2 Å, 4 Å, and 8 Å; (3)…”
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “To overcome some of the limitations of RMSD in the context of CASP, the Global Distance Test (GDT) was introduced in CASP4 (Zemla, 2003; Zemla et al., 2001).”
Improved protein structure refinement guided by deep learning based accuracy estimation (2020, background): “test - tertiary structure) (14) generated by homology modeling (15), trRosetta (1), and native structure perturbation (see Methods).”
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “When the procedure was applied topredictionsfrom theCASP10 experiment, thestruc-tureswerepresuperposedusing theprogramLGA(Zemla,2003),andnoaddi-tional superposition was performed.”
Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “Accuracy of prediction of 3D structure is quantified in 3 ways: (i) using the TM score [53]; (ii) using GDT-TS [54]; and (iii) using the Pymol [81] ‘align’ routine, which reports the Ca-RMSD for a moderately trimmed set of residues after iteratively removing the worst residue pairs from consideratio”
3D structures of membrane proteins from genomic sequencing (2012, positive): “Structures are additionally clustered using MaxCluster (Siew et al., 2000) single-linkage clustering to eliminate high-ranked outliers belonging to small clusters.”
High resolution comparative modeling with RosettaCM (2013, methodology): “The accuracy of the modeled protein backbone was assessed using the GDT(Zemla et al., 1999), the accuracy of the sidechain placements by the GDC-SC(Zemla, 2003), and the accuracy of the polar interactions by the fraction of recovered native hydrogen bonds (see Supplementary Information for detailed ”
High‐accuracy protein structure prediction in CASP14 (2021, neutral): “…(1) GDT_HA, the high-accuracy version of the Global Distance Test (GDT), rewarding parts of the target that could be reproduced with high precision 3 ; (2) lDDT, a local difference distance test that evaluates how well the all-atom distance map of the target is reproduced by the model 17 ; (3)…”
Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIV (2021, methodology): “Traditionally, CASP has used the multi-superposition, multiscale GDT_TS measure of agreement between models and experiment as a more robust metric than traditional RMSD when dealing with medium or poor-quality models.(23,24) In CASP 14, almost all best models are in close enough agreement with exper”