CASP13 Target Classification into Tertiary Structure Prediction Categories

By Lisa N. Kinch, Andriy Kryshtafovych, Bohdan Monastyrskyy, Nick V. Grishin. 2019

33 citations recorded by the source corpus.

Protein target structures for the Critical Assessment of Structure Prediction round 13 (CASP13) were split into evaluation units (EUs) based on their structural domains, the domain organization of available templates, and the performance of servers on whole targets compared to split target domains. Eighty targets were split into 112 EUs. The EUs were classified into categories suitable for assessment of high accuracy modeling (or template‐based modeling [TBM]) and topology (or free modeling [FM]) based on target difficulty. Assignment into assessment categories considered the following criteria: (a) the evolutionary relationship of target domains to existing fold space as defined by the Evolutionary Classification of Protein Domains (ECOD) database; (b) the clustering of target domains using eight objective sequence, structure, and performance measures; and (c) the placement of target domains in a scatter plot of target difficulty against server performance used in the previous CASP. Generally, target domains with good server predictions had close template homologs and were classified as TBM. Alternately, targets with poor server predictions represent a mixture of fast evolving homologs, structure analogs, and new folds, and were classified as FM or FM/TBM overlap.

Subfields: Materials Chemistry, Molecular Biology

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

Citations in the corpus

Assessment of Protein Model Structure Accuracy Estimation in CASP13: Challenges in the Era of Deep Learning (2019, methodology): “Assessment of local accuracy estimation was performed at the level of evaluation units (EUs).(15) Five EUs, T0960-D1, T0960-D4, T0963-D1, T0963-D4, and T0980s2-D1, for which hydrophobic core is absent within the monomer structure and oligomeric contacts seem to be critical for structure formation, w”
Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges (2021, methodology): “The local accuracy estimation was assessed at the level of evaluation units (EUs).(18) Two EUs from obligate oligomers, T1070-D1 and”