MaxSub: an automated measure for the assessment of protein structure prediction quality

By N. Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer. 2000

394 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, neutral): “In contrast to the protein structure prediction field, where there are several widely accepted quality measures; e.g., C α -RMSD, GDT_TS [3], MaxSub [4], TM-score [5], and S-score [6], the IS-score [7] for assessing protein complex models has not achieved wide adoption by the field and the current…”
Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “8 Å for at least 75% of the residues, using the accepted practice of omitting a moderate fraction of badly fitting residues in order to avoid exaggerated influence from outliers resulting from the square in the definition of Ca-RMSD (using the MaxCluster suite [62]).”
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.”
Pcons: A neural‐network–based consensus predictor that improves fold recognition (2001, methodology): “1999), MaxSub (Siew et al. 2000), and sf4 (Lackner et al.”
Protein homology detection by HMM?CHMM comparison (2005, methodology): “Here we employ a more direct approach, developed for the automatic assessment of structure prediction servers (Siew et al., 2000), where the generation of a structure-based sequence alignment is omitted as an intermediate step.”
Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins (2021, methodology): “Finally, a protein structure comparison and clustering tool called MaxCluster [42] was used to calculate the TM-scores of Set A and Set C.”
CONFOLD2: improved contact-driven ab initio protein structure modeling (2017, methodology): “SCRATCH suite [9] is used to predict three-state secondary structure and Maxcluster [10] to compute pairwise model similarity for clustering.”
The Phyre2 web portal for protein modelling, prediction and analysis (2015, methodology): “Superposition is performed using the MaxSub algorithm 33 .”
SphereGrinder - reference structure-based tool for quality assessment of protein structural models (2015, background): “MaxSub [4] is similar to GDT, but deals only with one particular threshold.”
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation (2003, methodology): “When assessed by a variant of MaxSub, 19 which uses RMSD as the threshold, the ﬁve submitted models were similar to those picked by the standard protocol alone (Table I).”
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model (2008, methodology): “MaxSub score [37] between the predicted (model) structure and the native structure is a measure of similarity between 0.0 (no similarity) and 1.0 (perfect similarity).”
3D Protein Structure Predicted from Sequence (2011, neutral): “8Å for at least 75% of the residues (using the accepted practice of omitting a moderate fraction of badly fitting residues in order to avoid exaggerated influence from outliers resulting from the ”