Drug Docking with Schrodinger

Overview

Instructor: Xin Yang

Time: Friday, February 11, 1:30PM-4:00PM

Location: Blocker 220 and online using Zoom

Prerequisites: HPRC account, basic Linux, and Molecular Biochemistry knowledge

This course introduces the basic concepts behind computer-aided drug design (CADD) with an emphasis on structure-based virtual screening. Docking predicts the preferred orientation of a ligand relative to a receptor and is one of the most frequently used methods for structure-based virtual screening. Docking results can allow users to quickly screen a large ligand database and take a subset of compounds with good docking scores for further evaluation with more computationally expensive, but scientifically rigorous calculations. In this course, you will learn how to generate a protein receptor grid, dock a set of ligands into the receptor, analyze protein-ligand poses, and filter compounds based on docking scores and other properties.

Course Materials

Presentation slides

The presentation slides are available as downloadable PDF files.

  • Drug Docking with Schrödinger (Spring 2022): PDF
  • Pre-class instructions (Spring 2022): PDF

  • Drug Docking with Schrödinger (Fall 2021): PDF
  • Drug Docking with Schrödinger (Spring 2021): PDF
  • Drug Docking with Schrödinger (Fall 2020): PDF
  • COVID-19 Drug Docking with AutoDock and Schrödinger (Spring 2020): PDF

Agenda

This course focuses on the following topics:

  • General workflow of computer aided drug design (CADD)
  • Basic concepts behind structure-based drug design
  • Ligand and protein preparation for ligand-receptor drug docking
  • Scoring functions
  • Hands-on exercises using Glide and CovDock

This course focuses on the basic concepts behind ligand-receptor drug docking using Schrödinger’s Glide and CovDock packages.