Glossary

FORM

Idealized secondary structure lattice representation of a protein structure. FORMS describe a layered topology in which each layer is composed of a defined number of either alpha-helices or hydrogen-bonded beta-strands. This compressed definition of the protein space was firstly introduced by Tylor and collaborators [Tay02], [TBC+08].

MASTER

The Method of Accelerated Search for Tertiary Ensemble Representatives takes as query a structural fragment composed of one or more disjoint segments and provably finds all fragments from a database matching the query to within a given RMSD threshold. [ZG15].

SKETCH

3D representation of a protein structure (backbone atoms only) of a FORM.

[Tay02]

William R Taylor. A ‘periodic table’for protein structures. Nature, 416(6881):657, 2002.

[TBC+08]

William R Taylor, Gail J Bartlett, Vijayalakshmi Chelliah, Daniel Klose, Kuang Lin, Tom Sheldon, and Inge Jonassen. Prediction of protein structure from ideal forms. Proteins: Structure, Function, and Bioinformatics, 70(4):1610–1619, 2008.

[ZG15]

Jianfu Zhou and Gevorg Grigoryan. Rapid search for tertiary fragments reveals protein sequence–structure relationships. Protein Science, 24(4):508–524, 2015.