Open-Source Tools for Chemists

These workshops offer a further opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry. All software and training materials required for the workshop will be provided for attendees to install and run on their own computers.

There are three two-hour sessions in this workshop series, which will be run on Zoom. All workshops are free to attend, but registration is required.

PDBe Knowledge Base
with David Armstrong, EMBL-EBI
 
This workshop explores the Protein Data Bank in Europe Knowledge Base (PDBe-KB https://www.ebi.ac.uk/pdbe/) resource and its tools for the investigation, analysis, and interpretation of biomacromolecular structures. PDBe-KB brings together data from all PDB entries and displays this data as aggregated information for individual proteins, including ligand binding sites, macromolecular interactions and more. Furthermore, this community-led resource brings together structural and functional information from a host of other related resources.

In this workshop, you will learn how to use the PDBe-KB aggregated views for proteins to investigate structural and function information for proteins and their associated ligands. We will also demonstrate effective use of novel visualisation components of large-scale structural data on these pages, including 3D visualisation of superposed protein structures with their bound ligands.

Further sessions in the series:

19 May 2022
KLIFS database 
with Albert Jelke Kooistra, Copenhagen University, and Andrea Volkamer, Charite Universitaetsmedizin, Berlin

KLIFS is a kinase database that dissects experimental structures of catalytic kinase domains and the way kinase inhibitors interact with them. The KLIFS structural alignment enables the comparison of all structures and ligands to each other. Moreover, the KLIFS residue numbering scheme capturing the catalytic cleft with 85 residues enables the comparison of the interaction patterns of kinase-inhibitors, for example, to identify crucial interactions determining kinase-inhibitor selectivity.  The workshop will be in two segments: 1) an introduction to KLIFS and 2) programmatic access and applications of KLIFS.

23 June 2022
Scoring of shape and ESP similarity 
with Esther Heid, Technical University of Vienna

Electrostatic effects along with volume restrictions play a major role in enzyme and receptor recognition. Evaluating electrostatic and shape similarities of pairs of molecules such as proposed versus known ligands can therefore be valuable indicators of prospective binding affinities. This workshop will demonstrate how to compute electrostatic and shape similarities using the open-source tool ESP-Sim (github.com/hesther/espsim, doi.org/10.26434/chemrxiv-2021-sqvv9-v3). Available options for comparing electrostatics will be discussed interactively on selected examples of public datasets, along with advice on embedding and aligning molecules prior to computing similarities.