Ligand Designer

Intuitive, interactive 3D ligand design for hit-to-lead and lead optimization

Ligand Designer provides powerful, yet easy to use 3D visualization and ligand building capability that is scientifically proven while making it fun to design ligand modifications in 2D or 3D and see how those changes are likely to impact protein-ligand complex structures. Cutting through the complexity of visualizing 3D information, the Ligand Designer uses concepts from Augmented Reality to enable you to layer relevant information including a novel grow space to quickly recognize where ligand modifications are most desirable. 

The Ligand Designer democratizes the 3D design process by putting the power of common medicinal chemistry tactics at your fingertips.

Automated expert tools for chemists to easily design and evaluate ideas

Recognize and Displace Unstable Water
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2D to 3D Ideation
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Form Protein-Ligand Interactions
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Cyclize Ligands
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Benefits of Ligand Designer to Design and Evaluate Ideas

Choose your own adventure with manual or guided design to evaluate ideas. Common medicinal chemistry workflows are included so you can test ideas automatically and avoid information overload.

GUIDED DESIGN

Design in 2D and see the structures in the workspace; in 2½ D and see the representation of the binding pocket with key information; or design in 3D with full control.

DESIGN YOUR WAY

Easily assess the impact of ligand changes by visualizing the complex geometry while reducing the noise of un-needed information to find the next idea. Controls are pre-programmed to fit your function.

AUTOMATED EXPERT TOOLS

Tailor it to your chemistry of interest by using synthetically tractable enumeration or R-group enumeration.

TAILOR CHEMISTRY TO YOUR PROJECT

Glide docking, automated ideation using R-group libraries or Pathfinder, Prime’s Macrocycle, BREED and WaterMap are all used in Ligand Designer.

POWERFUL BUILT-IN TECHNOLOGY

Rationalize SAR, drive potency and tune selectivity using WaterMap to compute the entropy and enthalpy of “hydration sites.”

A MAP TO STABLE WATERS

Overview of Ligand Designer

Features
Highlights
Demo

Additional Workflows

Training Materials

Forming Protein-Ligand Interactions with the Ligand Designer

In this tutorial you will learn how to use the Ligand Designer to optimize a hit molecule with protein-ligand interactions

WaterMap-Guided Lead Optimization with the Ligand Designer

In this tutorial, you will learn how to use the Ligand Designer to optimize a hit molecule using WaterMap- guided lead optimization.

FIND MORE HELPFUL RESOURCES IN THE TRAINING CENTER

Publications

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

Repasky, M.P.; Murphy, R.B.; Banks, J.L.; Greenwood, J.R.; Tu- bert-Brohman, I.; Bhat, S.; Friesner, R.A.,S.B.; Troast, D.M.; Abel, R.; Friesner, R.A.

J. Comput-Aided Mol. Des., 2012View
Calculating Water Thermodynamics in the Binding Site of Proteins— Applications of WaterMap to Drug Discovery

Cappel, D.; Sherman, W.; Beuming, T.

Curr Top Med Chem., 2017View
Reaction-based Enumeration, Active Learning, and Free Energy Calculations to Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin Dependent Kinase 2 Inhibitors

Konze, K.; Bos, P.; Dahlgren, M.; Leswing, K.; Tubert- Brohman, I.; Bortolato, A.; Robbason, B.; Abel, R.; Bhat, S.

ChemRxiv, 2019, PreprintView

Supercharge your design and evaluation of ideas with Ligand Designer

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