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OpenCADD-KLIFS: Sync stat. of need in paper with docs (issue #124) #131

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Dec 7, 2021
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OpenCADD-KLIFS: Sync stat. of need in paper with docs (issue #124) #131

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4 changes: 3 additions & 1 deletion paper/paper.md
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Expand Up @@ -30,14 +30,16 @@ The OpenCADD-KLIFS Python module offers a convenient integration of the KLIFS da

# Statement of need

[OpenCADD-KLIFS](https://opencadd.readthedocs.io/en/latest/databases_klifs.html) (``opencadd.databases.klifs``) is a part of the [OpenCADD](https://opencadd.readthedocs.io/) package, a collection of Python modules for structural cheminformatics.
OpenCADD-KLIFS is aimed at current and future users of the KLIFS database who seek to
integrate kinase resources into Python-based research projects.
This module offers access to KLIFS data [@Kanev:2021] such as information about kinases, structures, ligands,
interaction fingerprints, and bioactivities.
KLIFS thereby focuses especially on the ATP binding site, defined as a set of 85 residues and aligned across all structures using a multiple sequence alignment (MSA) [@vanLinden:2014].
With OpenCADD-KLIFS, KLIFS data can be queried either locally from a KLIFS download or remotely from the KLIFS webserver.
The presented module provides identical APIs for the remote and local queries for KLIFS data and streamlines all output into
standardized Pandas DataFrames [@pandas] to allow for easy and quick downstream data analyses (\autoref{fig:opencadd_klifs_toc}). This Pandas-focused setup is ideal to work with in Jupyter notebooks [@Kluyver:2016].

[OpenCADD-KLIFS](https://opencadd.readthedocs.io/en/latest/databases_klifs.html) (``opencadd.databases.klifs``) is a part of the [OpenCADD](https://opencadd.readthedocs.io/) package, a collection of Python modules for structural cheminformatics.

![OpenCADD-KLIFS fetches KLIFS data [@Kanev:2021] offline from a KLIFS download or online from the KLIFS database and formats the output as user-friendly Pandas DataFrames [@pandas].\label{fig:opencadd_klifs_toc}](opencadd_klifs_toc.png)

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