Open-Source Tools workshops
Registration for the next batch of Open-Source Tools workshops run by the RSC Chemical Information and Computer Applications Group is now open.
These workshops have been enormously popular and the interactions with the instructors have been especially valuable. Details of the next 3 workshops are described below.
All meetings start at 2 pm UK time (5 min break after 1 hour). All run using Zoom Webinar
21 April 2022 PDBe Knowledge Base (David Armstrong)
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.
19 May 2022 KILFS database (Albert Jelke Kooistra, Andrea Volkamer )
Over the past three decades, six thousand structures of the catalytic kinase domain have been made publicly available via the Protein Data Bank. But to what extent are we making use of this wealth of information? In order to harness this data in a better way and to make it readily available for all to use in their research, KLIFS (https://klifs.net) was constructed. KLIFS, i.e. the Kinase–Ligand Interaction Fingerprints and Structures database, is a structural kinase database that systematically collects and processes all structures of the catalytic kinase domain. With the database, you can - for example - easily get a complete overview of all structures, search for ligands with a specific binding mode, identify analogs or your ligands of interest, collect data for your data mining and machine learning applications.
For this workshop, the developers of KLIFS have teamed up with the Volkamer Lab and therefore the workshop will be divided into two segments. First, Albert J. Kooistra will give an introduction to KLIFS and demonstrate different functionalities of the KLIFS website and the integration of KLIFS in KNIME via the 3D-e-Chem nodes. In the second half, Andrea Volkamer and Dominique Sydow will demonstrate, based on their new kinase-focused TeachOpenCADD workflow, how to assess kinase similarity from different data perspectives. They will emphasize their Python package KiSSim – a KLIFS-based kinase structural similarity fingerprint, and OpenCADD-KLIFS – a Python module to facilitate the integration of KLIFS data into kinase research workflows.
23 June 2022 Scoring of shape and ESP similarity (Ester Heid)
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.