Workshops

Workshop 1 (Monday 15:00 & Tuesday, 14:30): OpenEye toolkits

In this workshop we will explore usage of the OpenEye toolkits to solve some standard problems in cheminformatics and drug discovery. Toolkits provide a very efficient and easy to use layer of programming support for chemoinformatic tasks from file conversion to molecular manipulations to protein prep, virtual screening and more. Toolkits allow deeper access to methods otherwise exposed in finished applications built and optimized for a single purpose. Such single-purpose tools include all your downloadable applications from software vendors. While they might expose some parameters to adjust, the underlying methods are set. 

In addition to writing your own version of such tools without reinventing the wheel, toolkits are a great help optimizing throughput and stripping away the need of writing output to disk between operation. With the help of Jupyter notebooks we will showcase the utility of OpenEye Toolkits. These toolkits are free to use for academic users – simply contact us if you want to continue using the toolkits after the end of the workshop.

Workshop 2 (Wednesday, 15:00): The ORION™ platform

Participants will get a chance to explore a fully Cloud-based platform to help solve drug discovery problems. The ORION™ platform allows for easy-to-use, re-usable flow-based protocols to run at any scale. 

In a structure-enabled project these tasks can include:

• preparing one or multiple proteins, 
• preparing (large numbers of) ligands in 3D (Enamine REAL 24.4B molecules is ready to use),
• docking ligands to the protein, 
• clustering results, 
• running relative-binding free energy calculation, 
• and much more…

Results can be analyzed interactively in different chart plots, 3D visualizations and they can be shared with colleagues. In a hands-on exercise you will be able to explore some of these capabilities yourself.

Session 1 (15:00 – 16:30): Molecular Field Alignment in Structure-Based Drug Discovery

In the first session, we focus on how molecular field alignment can enhance structure-based drug discovery, using the JAK kinase family as a representative example of a highly conserved target system. Participants will learn how traditional docking approaches often struggle in such systems due to the similarity of ATP-binding pockets, leading to incorrect poses and poor prioritization. We introduce an interaction-driven paradigm, where electrostatic and hydrophobic fields derived from crystallographic ligands are used to guide pose generation and improve scoring. Through two practical cases

1. regenerating initial docking poses driven by crystallographic ligand alignment and
2. scoring docking poses based on alignment with the reference ligand

participants will gain hands-on insight into how field-based methods can better capture the subtle interaction patterns that govern binding and selectivity.

Session 2 (17:00 – 18:30): Coupling synthon-based searches with D2B experimental screening

The second session demonstrates how integrating Pharmscreen and Exascreen into a fragment-to-hit pipeline enables more efficient hit discovery and expansion while significantly reducing experimental costs. Starting from fragment screening, molecular field alignment is used to prioritize a reduced subset of compounds with a high likelihood of activity, followed by the identification of compatible synthons that preserve key interaction patterns and growth vectors. Finally, virtual synthon expansion allows rapid exploration of chemical space and prioritization of compounds before synthesis. This integrated approach shows how field-based methods can guide decision-making across multiple stages—from fragment selection to hit expansion—ultimately improving hit rates while minimizing experimental effort.