X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy.

ABSTRACT: X-Entropy is a Python package used to calculate the entropy of a given distribution, in this case, based on the distribution of dihedral angles. The dihedral entropy facilitates an alignment-independent measure of local protein flexibility. The key feature of our approach is a Gaussian kernel density estimation (KDE) using a plug-in bandwidth selection, which is fully implemented in a C++ backend and parallelized with OpenMP. We further provide a Python frontend, with predefined wrapper functions for classical coordinate-based dihedral entropy calculations, using a 1D approximation. This makes the package very straightforward to include in any Python-based analysis workflow. Furthermore, the frontend allows full access to the C++ backend, so that the KDE can be used on any binnable

SUBMITTER: Kraml J 

PROVIDER: S-EPMC8154256 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature