A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort.

ABSTRACT: Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems. Here we present a new paradigm for MD databases, resilient to large systems and long trajectories, and designed to be compatible with modern MD simulations. The data are offered to the community through a web-based graph

SUBMITTER: Beltran D 

PROVIDER: S-EPMC10767965 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature