The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers.

ABSTRACT: Understanding of the structural and dynamic behaviour of molecules is a major objective in molecular modeling research. Sampling through the torsional space is an efficient way to map their behaviour. However, generating a landscape of possible conformations relies on multiple formalisms whose mathematics are often difficult to convert to code. Here we present a command line tool and a scripting module to provide the means to generate such landscapes with different axes according to various formalisms exploited for conformational sampling. Additionally to this toolkit, we apply a benchmarking study on subjecting a DNA nucleoside to a diverse set of quantum mechanical levels of theory for geometry optimisations and energy potential calculations. The potential of the tool is demonstrated on

SUBMITTER: Rihon J 

PROVIDER: S-EPMC12007234 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature