A topological data analytic approach for discovering biophysical signatures in protein dynamics.

ABSTRACT: Identifying structural differences among proteins can be a non-trivial task. When contrasting ensembles of protein structures obtained from molecular dynamics simulations, biologically-relevant features can be easily overshadowed by spurious fluctuations. Here, we present SINATRA Pro, a computational pipeline designed to robustly identify topological differences between two sets of protein structures. Algorithmically, SINATRA Pro works by first taking in the 3D atomic coordinates for each protein snapshot and summarizing them according to their underlying topology. Statistically significant topological features are then projected back onto a user-selected representative protein structure, thus facilitating the visual identification of biophysical signatures of different protein ensembles.

SUBMITTER: Tang WS 

PROVIDER: S-EPMC9098046 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature