Small molecules and their protein targets: interactions, function, and classification

Small molecules (or chemicals) play a crucial role in biological systems, acting as precursors to macromolecules, cells, and tissues. Beyond this, they are involved in cell signalling, regulation, energy consumption and production, and can be used therapeutically to treat diseases. 

To understand the role of chemicals in a biological context, we can study how they bind to and impact the function of their macromolecular targets, such as DNA, RNA, and protein. To better capture and standardise the nature of the chemical-protein interactions, and to place these in a broader context, we can use relevant annotations and classifications.

This six-hour virtual workshop offers hands-on experience with EMBL-EBI tools and resources to explore the biological interactions of small molecules with protein targets. Using case studies, we will guide you through workflows to investigate drug interactions with a protein target, and to standardise and annotate these interactions using dedicated protein and chemistry classification resources. 

We will primarily use ChEMBL to identify small molecule drugs and experimental data describing their impact on targets and PDBe to evaluate target binding details. To classify these compound-protein interactions, we’ll use ChEBI and UniProt for chemical and protein annotations, respectively.

Virtual course
This course will take place on Zoom. Trainers will be available to assist during practical sessions, answer questions, and provide further explanations during the Zoom. 

To join the course, you will need to create a free EMBL-EBI Training website account.

Who is this course for?

This course is aimed at wet-lab scientists, such as cell biologists, enzymologists, biochemists and medicinal chemists, as well as bioinformaticians and those exploring cheminformatics. It is designed for those who would like to use EMBL-EBI data resources to interpret the effects of small-molecule drugs binding to a biological target. No programming experience is required.

What will I learn?

Course content

During this course, you will learn about:

• Bioactivity data for drugs and drug-like molecules contained in ChEMBL.
• Linking drug targets in ChEMBL to their ligand-protein structures in PDBe.
• Experimental and predicted structures for a given protein in PDBe.
• Cross-referencing to ontologies and annotation of ligand-target structures with controlled vocabulary and identifiers. 

Learning outcomes

After the course, you should be able to:

• Extract small molecule drug data from ChEMBL, including database accessions, structural representations, physicochemical properties, and drug targets/indications.
• Identify experimental structures using PDBe and interpret the drug-target binding interactions.
• Classify and standardise the ligand-target structures using annotations from ChEBI and UniProt.

Trainers

Places will be allocated on a first-come first-served basis, so please register soon to avoid disappointment. Registrations will close on 10 August 2026, or when places are filled. Incomplete registrations will not be processed.