Processing and evaluation of predictions in CASP4

By Adam T. Zemla, Č. Venclovas, John Moult, Krzysztof Fidelis. 2001

161 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy, Evaluation & Benchmarks, Computational Biology & Bioinformatics

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

In Molecular Biology

In Spectroscopy

In Evaluation & Benchmarks

In Computational Biology & Bioinformatics

Citations in the corpus

Learning from Protein Structure with Geometric Vector Perceptrons (2020, background): “GDT-TS is a scalar measure of how similar two protein backbones are after global alignment (Zemla et al., 2001).”
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”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, methodology): “We evaluated the model quality of a decoy using the widely used Global Distance Test (GDT; Zemla, 2003; Zemla et al., 1999, 2001), which compares a decoy with its native and generates a quality value between 0 and 100.”
Evaluation of the template-based modeling in CASP12 (2017, methodology): “To measure alignment accuracy, we compute the AL0 score, 2,25 representing the number of correctly aligned residues in the LGA 4 Å superposition of the modeled and experimental structures.”
Assessment of chemical-crosslink-assisted protein structure modeling in CASP13 (2019, methodology): “To assess accuracy of crosslinking-assisted models and their improvement over the corresponding non-assisted predictions, we employed the GDT_TS measure 18,19 for monomeric predictions, and the LDDT measure 20 for multimeric ones.”
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison (2010, methodology): “To evaluate the quality of the models we use the template modeling score (TM-score) [25], which is similar to GDT_TS [31] and MaxSub [32] measures, but is designed to be less dependent on the protein size.”
CAD‐score: A new contact area difference‐based function for evaluation of protein structural models (2013, methodology): “4,5 The new CAD-score uses a more accurate algorithm for the contact area calculations.”
The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes (2014, methodology): “δ(i ) = ∑ (i, j )∈G min(|T(i, j ) − M(i, j )|, T(i, j )) (2)”
Critical assessment of methods of protein structure prediction (CASP)‐round V (2003, methodology): “All submissions were processed by the Prediction Center at the Lawrence Livermore Laboratory.(21) Accepted submissions were issued an accession number that served as the record that a prediction had been made by a particular group on a particular target.”
Evaluation of template-based modeling in CASP13 (2019, methodology): “While torsion-based analyses have been previously used in assessing CASP rounds 3, 8 4 9 and 9 10 they have not been widely adopted — perhaps because such metrics only become truly meaningful once the majority of the fold is essentially correct.”