ArticleJournal of cheminformatics2017
Scoria: a Python module for manipulating 3D molecular data.
Article in Journal of cheminformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.bioRxiv : the preprint server for biology · 2022Article
- LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates.Journal of cheminformatics · 2020Article
- AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization.Journal of cheminformatics · 2020Article
- Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.Journal of cheminformatics · 2019Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .
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