De Novo Design with
Discovery Studio - Training

Overview - De Novo Design with Discovery Studio - Training

De novo design identifies potential novel ligands by screening a library of small molecules to find those that are complementary to a target receptor. In this workshop, participants will learn about using the De Novo Design protocols present in Discovery Studio. Ludi, a de novo design program, will be discussed and be applied to fit fragments into the active site of a receptor. The program AutoLudi will be applied to identify and fuse small fragments into a starting scaffold to construct a growing ligand.

On completion of the workshop the user will have covered:

Examination of a protein receptor and define its binding sites
Generation of an interaction site map for use in fragment fitting
Setting up the De Novo Receptor and Link mode protocols for running Ludi
The De Novo Evolution protocol that uses the program AutoLudi, to fuse small fragments for constructing novel ligand structures
Running De Novo Evolution protocol in different modes to vary the nature of fragment selection and construction of new molecules
Performing in situ minimization of constructed ligands in the protein binding site
Customizing existing fragment libraries for use in the de novo design protocols in Discovery Studio

Sample Agenda

Web-based Course

Welcome
Overview of De Novo Design in Discovery Studio (Lecture) (15 min)
De Novo Design using Ludi (Lecture and Demo) (110 min)
Break (10 min)
De Novo Evolution (Lecture and Demo) (50 min)
Q &A (10 min)

On-site Course

09:00 - 09:15: Welcome and Administration Announcements
09:15 - 09:30: Overview of De Novo Design (Lecture)
09:30- 10:30: De Novo Design (Lecture)
10:30 - 10:45: Break
10:45 - 11:15: De Novo Design (Lecture)
11:15 - 12:30: De Novo Design (Hands-On)
12:30 -13:30: Lunch
13:30- 14:30: De Novo Evolution (Lecture)
14:00 - 14:45: De Novo Evolution (Hands-On)
14:45 - 15:15: De Novo Evolution (Hands-On)
15:15 - 15:30: Break
15:30 - 16:00: Open Discussion