Introduction to computational tools for molecule design

November 27, 2017 • New Delhi, India

13:45 Registration
14:00 Introduction to Cresset
14:15 SAR with Forge
15:00 Break
15:15 Spark: discover new directions for your project using bioisosteres
16:00 Structure-based design with Flare
16:45 Questions
17:00 Close


Designing new molecules based on a deep understanding of SAR with Forge

Using the Activity Atlas models and the innovative Activity Miner interface of Forge, you will learn how to rapidly decipher the SAR of a series of molecules. I will highlight an efficient workflow, detail how to identify outliers and generate meaningful summaries of SAR for use in molecular design in Torch or Forge.

Scaffold hopping to new cores and R-groups using Spark

Using Spark I will show how you can quickly generate novel ideas for your project by scaffold hopping or using bioisosterism in R-group selection. I will introduce the standard functionality of Spark with an emphasis towards new users. You will learn about the choice of databases to search, how to link searches and results to available reagents, visualization and interpretation of results and selection/tagging/filtering of the best molecules to progress.

Accessible, advanced structure-based design with Flare

The completely novel Flare interface makes structure based design accessible and easy but also gives access to cutting-edge advanced scientific methods. I will show how the key capabilities of Flare are applicabile to small molecule discovery projects with a focus on molecular design. You will learn basic tasks such as sequence alignment and superimposition of proteins, docking, minimization of protein-ligand complexes with the XED force field, and molecule design in the context of the active site. I will introduce calculation of the electrostatics of the protein active site, calculations of water stability and locations using 3D RISM, and energetics of ligand binding using WaterSwap.

About the presenter, Dr Rae Lawrence

Following a PhD in theoretical chemistry from the University of Missouri-Columbia, Rae held scientific and account management roles at Chemical Computing Group, CompuDesign Group and Advanced Chemistry Development (ACD/Labs). Rae joined Cresset in 2010. She is responsible for providing applications science in support of the account managers for North America and India and encourages a collaborative approach to workings with customers.

Rae has publications in nociception, HIV, and a provisional patent in agrochemistry.


Room No. 002, School of Computational and Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi – 110067, India