SI2012 Computer Aided Drug Discovery Pipeline

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Molecular Dynamics Simulations: Students will learn the basics of MD simulation with NAMD using their own experimental system(s). Key input files and their preparation will be introduced.


Docking Basics, Ensemble Structure Selection & Ensemble Docking: Students will get an introduction to docking and the general concepts used, along with some workflow/algorithms used in virtual screening workflows. RMSD-based cluster and QR factorization will be presented as tools to identify distinct receptor conformations using clustering methods such as RMSD-based clustering and QR factorization. Elementary methods of ensemble docking will be presented.

CADD pipeline is being refactored with a new user interface, so the following tutorials are provided only as a reference.

  1. 2011 CADD Clustering Tutorial
  2. 2011 CADD QR factorization tutorial
  3. 2011 CADD Multiple receptor virtual screening


Analyzing and Improving Virtual Screening Performance: The basics of statistical performance analysis as a validation tool will be discussed in the context of ensemble virtual screens. Students will learn to visualize virtual screening results, perform basic interaction analysis and rescoring. Best practices and validations will be discussed.


Ligand Library Preparation, Hit Analysis and Compound Selection: Discussion of cheminformatic practices to develop a target-focused small molecule library for docking & subsequent compound selection be presented. Students are welcome to bring their own project files for assistance during this session.


New CADD Applications: Ensemble-based "hot spot" mapping using FTProd is introduced, followed by a brief introduction to more rigorous free energy methods. After a coffee break, lead optimization using AutoClick, AutoGrow, and LigMerge tools will be illustrated.

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