Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off.

ABSTRACT: The recent breakthrough in the field of protein structure prediction shows the relevance of using knowledge-based based scoring functions in combination with a low-resolution 3D representation of protein macromolecules. The choice of not using all atoms is barely supported by any data in the literature, and is mostly motivated by empirical and practical reasons, such as the computational cost of assessing the numerous folds of the protein conformational space. Here, we present a comprehensive study, carried on a large and balanced benchmark of predicted protein structures, to see how different types of structural representations rank in either accuracy or calculation speed, and which ones offer the best compromise between these two criteria. We tested ten representations, including low-res

SUBMITTER: Postic G 

PROVIDER: S-EPMC8120936 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature