Course Description

This course concentrates on both ligand-based and structures-based virtual screening of molecules.  When the receptor structure is not known, a set of active ligands is aligned, and the aligned set of compounds is used as a similarity template to find other molecules with similar shapes and placement of features.  When the receptor structure is known, ligands are screened by docking them into the receptor. 

Who Should Attend

Chemists and biologists who screen large sets of compounds for lead identification.

Requirements

Before attending this course, participants should be able to perform the following tasks in SYBYL: Manipulate molecules with a mouse, create molecular spreadsheets, add columns to molecular spreadsheets, display structures from molecular spreadsheets, and prepare protein-ligand complexes. These topics are covered in the courses Getting Started with SYBYL-X and Modeling Proteins and Ligands .

What You Will Learn

• Perform lead-hopping using shape-based searching.
• Use similarity to find promising ligands when no receptor structure is available.
  
• Use docking to find promising ligands when a receptor structure is available.
• Increase the percentage of actives in your datasets by eliminating poorly binding compounds.

Course Topics

Course Objectives

1. Find molecules with similar shapes to a query structure.
2. Create a template of aligned active compounds to be used for screening purposes.
3. Identify compounds with the most favorable scores when aligning to a template.
4. Display the binding site of a ligand-receptor complex with hydrogen bonds indicated between the ligand and the receptor.
5. Dock a set of molecules into a defined receptor site.
6. View poses of docked ligands in a receptor site, and identify the compounds with the most favorable scores.

Modules Used

SYBYL-X (Biopolymer, CSCORE, Surflex-Dock, Surflex-Sim, and Topomer Search).

Course Length

1 day

Pricing Information

Tripos, Inc. reserves the right to modify course content at any time without prior notice.