University College Dublin Computational Chemistry Summer School


Cresset, BiOrbic, Bioeconomy SFI Research Centre, Crystal3 MSCA Consortium, SSPC, SFI Research Centre for Pharmaceuticals, MedChemica, and University College Dublin are delighted to present the second year of this state-of-the-art computational chemistry course focused on the life and chemical sciences. This two-day, free, interactive event will encompass several areas within the field and will provide a flexible learning platform to attendees from a wide range of interest areas including chemistry, biology, biochemistry, pharmaceutical sciences, veterinary sciences and agriscience. 

While no prior knowledge of computational chemistry is required, we will also have opportunities for those with experience to further their understanding. Parallel learning streams will be provided for both biology and chemistry backgrounds.

Please find registration at the bottom of the page.

Who should attend by organization?

Registrations are welcome from all those working in life sciences research, but are particularly encouraged from University College Dublin and sponsor organizations, including affiliated higher education institutes, industry and academic spin-outs.

Who should attend by role?

Academics • Postgraduate students • Undergraduate students • Research scientists • Technical staff 

Poster showcase

Poster and networking sessions will be held on Tuesday 6th June to give the opportunity for attendees to showcase their research. All posters will be hosted online in addition to the opportunity to present these in-person on the day. Prizes will be given to selected, outstanding posters based on the decision of the reviewing committee. Please note that poster submission is for in-person attendees only. 

Tuesday 6th June: Scientific Program

This will be a hybrid day with the option to join in-person or virtually. There is a limit to in-person places, these will be given on a first-come-first-served basis. 

Time (BST) Session Title Presenter
09:00 Registration

Welcome and Sponsor Introduction

Morgan Morris

Postdoctoral Scientist, Cresset


Introduction to Computational approaches within the Life Sciences

Nathan Kidley

Principal Application Scientist, Cresset


Predicting how my new molecules will behave

Oliver Hills

Postdoctoral Scientist, Cresset

11:00 Poster Session and Networking Break
12:00 Medicinal Chemistry is a Game of Matched Pairs

Al Dossetter

Managing Director, MedChemica

12:35 How do I model biological targets, and how do I predict their interactions with my new molecules?

Scott Midgley

Application Scientist, Cresset

13:05 Lunch and Networking Break
14:00 Drug Discovery: The Big Picture 

Rob Young

Principal, Blue Burgundy

14:50 How do I generate new molecules for my research project?

Selma Sapmaz

Scientist, Cresset

15:20 Poster Session and Networking Break
16:00 Free Energy Perturbation in Life Sciences

Sofia Bariami

Associate Product Manager, Cresset

16:50 Poster Prizes
17:25 Networking Drinks Reception

Please find registration at the bottom of the page.


An introduction to computational chemistry and its application in life science research

Nathan Kidley, Principal Application Scientist, Cresset

Computational methods are a powerful tool in life science research, enabling teams to increase research efficiency and remove unnecessary wet lab work. Starting at the most basic level, we will introduce computational chemistry methods and how they are applied in life science research.

Predicting how my new molecules will behave

Oliver Hills, Postdoctoral Scientist, Cresset

Creating novel structures is just the first step in new molecule design: we also need to be able to predict physical properties and biological activities of our new molecules so that we can prioritize the right candidates. Specifically, we will explore how this is typically done in a drug discovery context.

Medicinal Chemistry is a Game of Matched Pairs

Al Dossetter, Managing Director, MedChemica

The medicinal chemistry process is data analysis and compound design. In order to understand the Structure Activity Relationships (SAR), two compounds are compared and the structural difference between them attributed to the change in measured property. These two compounds are a Matched Pair; so SAR is Matched Pair Analysis. The talk will describe Matched Pair Analysis and AI compound design systems.

How do I model biological targets, and how do I predict their interactions with my new molecules?

Scott Midgley, Application Scientist, Cresset

We will give an overview of how in silico methods can be used to understand complex systems, with a focus on protein modeling to predict properties and interactions with small molecules.

Drug Discovery: The Big Picture

Rob Young, Principal, Blue Burgundy

Leen Gorissen advocates “Building the future of innovation on millions of years of Natural Intelligence” in her book of this title. Rob's talk explores how such concepts influence drug discovery, supporting the notion that “The Time and Place for Nature in Drug Discovery” is now. Whilst natural product likeness is demonstrably falling in approved drugs, new data illustrate the emerging importance of pseudo natural products in their structures. These findings have profound implications for drug design and suggest Darwinian selection of successful molecules, rationalised by Natural Intelligence, yet amenable for computational methods to Augment Intelligence!

How do I generate new molecules for my research project?

Selma Sapmaz, Scientist, Cresset

Learn how computational chemistry can be used to generate innovative ideas for your project, ensuring that you escape the boundaries of in-house or published prior work. Examples will be given on how to generate novel structures relevant to chemical and biological problems.

Free Energy Perturbation in Medicinal Chemistry

Sofia Bariami, Associate Product Manager, Cresset

FEP is a way to predict how strongly two molecules bind together, based on their chemical properties and their shape. In essence, they measure the "stickiness" of a molecule to a target. By simulating the behavior of a drug molecule in the presence of the target, researchers can calculate the amount of energy released or absorbed as the two molecules bind together. The more energy released, the stronger the interaction between the two molecules, and the more likely the drug is to be effective. 

7th June • Workshops

Hands-on software workshops will run in two parallel sessions. Attendees will be provided with a 60-day free license to Flare™ and Spark™ ahead of the workshops. 

Please note that there are limited spaces for these workshops and they are for in-person attendance only. 



Track 1

Track 2

09:00 Crash-course Introduction to Softwares
09:45 Introduction to Flare: Chemistry and Biology applications
11:15 Networking Break
11:45 Intro to Spark and Intermediate Flare Intermediate Flare: Manipulating protein structure
13:15 Lunch break
14:15 The integrated workflow: Docking Spark results in Flare Advanced Flare: Modeling protein properties
15:45 Closing Remarks Closing Remarks

Please find registration at the bottom of the page.

Workshop abstracts

Introduction to Flare™: Chemistry and Biology applications

This will be an introductory guided tour of Flare, a comprehensive platform for molecular modeling and design. In this session, learn how to visualize and manipulate ligands and protein targets, change display types, investigate ligand-protein interactions, and create publication quality images.

Introduction to Spark™: Generating novel chemical structures

This will be an introduction to Spark, an R-group replacement and scaffold hopping tool. Learn how to modify existing molecules to avoid problems with structure yet retain activity or performance, including de novo design of novel, patentable compounds.

The integrated workflow: Docking Spark results into Flare

In this session, learn how to prioritize new molecule ideas. We will transfer the output from Spark into Flare in order to access a wider range of structure-based features which allow you to predict the properties of your new molecules.

Intermediate Flare: Manipulating protein structure

In this session, we will take a more in-depth look into the capabilities of Flare and show how these can be used to manipulate protein structure, predict properties and analyze protein-protein and protein-ligand interactions.

Advanced Flare: Modeling protein properties

Protein structures are complex and dynamic. They exist in solvated environments, e.g., surrounded by counter-ions and water molecules or they may be embedded in membranes. To model protein properties accurately, we need to consider the dynamic nature of the molecular system. Using Flare, we will show that you can visualize how proteins move over time and interact with their environment(s). As an example of an application of this, we will show how we can identify regions where water molecules can be displaced easily by an incoming ligand.

Event sponsors 

BiOrbic Cresset Crystal3 Consortium MedChemica SSPC UCD School of Chemistry
BiOrbic logo Cresset logo without tagline Crystal3 Logo MedChemica SSPC Logo UCD logo


University College Dublin campus, Belfield, Dublin 4, Ireland, D04 V1W8.


UCD Computational Chemistry Summer School 2023

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