TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research.

Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming-especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub.

Structure and Thermodynamics of Eu(III) and Cm(III) Complexes with Glucuronic Acid.

Complexation by small organic ligands controls the bioavailability of contaminants and influences their mobility in the geosphere. We have studied the interactions of Cm3+, as a representative of the trivalent actinides, and Eu3+, as an inactive homologue, with glucuronic acid (GlcA) a simple sugar acid. Time-resolved laser-induced luminescence spectroscopy (TRLFS) shows that complexation at pH 5.0 occurs only at high ligand to metal ratios in the form of 1:1 complexes with standard formation constants log ß0 = 1.84 ± 0.22 for Eu3+ and log ß0 = 2.39 ± 0.19 for Cm3+. A combination of NMR, QMMM, and TRLFS reveals the structure of the complex to be a half-sandwich structure wherein the ligand binds through its carboxylic group, the ring oxygen, and a hydroxyl group in addition to five to six water molecules. Surprisingly, Y3+, which was used as a diamagnetic reference in NMR, prefers a different coordination geometry with bonding through at least two hydroxyl groups on the opposite side of a distorted GlcA molecule. QMMM simulations indicate that the differences in stability among Cm, Eu, and Y are related to ring strain induced by smaller cations. At higher pH a stronger complex was detected, most likely due to deprotonation of a coordinating OH group.