Fast, efficient fragment-based coordinate generation for Open Babel.

ABSTRACT: Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task for cheminformatics and across a wide range of molecular modeling. Consequently, developing a fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce a fragment-based coordinate generation implementation for Open Babel, a widely-used open source toolkit for cheminformatics. The new implementation improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. Input molecules are broken into fragments by cutting at rotatable bonds. The coordinates of fragments are set according to a fragment library, prepared from open crystallographic databases. Since the

SUBMITTER: Yoshikawa N 

PROVIDER: S-EPMC6676618 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature