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Structure Based Design Training

Library Design

Duration: 1 day

Docking - Ligand fit, Libdock and CDocker

This workshop covers three different approaches to docking ligands in a protein active site:

Dock Ligands (LigandFit)- ligand conformations generated using Monte-Carlo techniques are initially docked into an active site based on shape, followed by further CHARMm minimization.

Dock Ligands (CDocker)- random ligand conformations are generated using  CHARMm based molecular dynamics. The positions of the ligands are optimized in the binding site using rigid body rotations followed by simulated annealing.

DockLigands(LibDock)- a high-throughput docking algorithm that positions Catalyst generated ligand conformations in the protein active site based on polar and apolar interaction sites (hotspots).

Lectures and accompanying exercises will focus on these docking protocols, including the calculation of binding energies, and the use of scoring functions to facilitate the ranking of docked ligands. In addition, analysis tools will be used that allow the visualization and charting of various protein ligand interactions, as well as the calculation of enrichment hit-rate plots and ROC curves.

Duration: 1 day

Advanced Docking - Flexible Docking/Constrainted Docking

This workshop will focus on two advanced docking protocols. The first, Flexible Docking, will address the inherent flexibility of the protein ligand complex. Both the lecture and related exercise will explore how Flexible Docking allows the amino acid side chains to adopt multiple conformations, as well as considering multiple ligand conformations during the docking phase.

The second approach to docking in this workshop (Dock Ligands (Pharmacophore Restraints and CHARMm) will employ a pharmacophore to constrain the ligand in the protein active site. Using either the protein structure itself, or a docked ligand as a template to build the pharmacophore, multi-conformer drug-type molecules can be docked into an active site using these 3D pharmacophore restraints as an initial screen.  The initial docking is followed by CHARMm simulated annealing optimization.

The course will take an in-depth look at the methodologies incorporated into these protocols , and allow the user to perform hands-on exercises to familiarize themselves with the workflows.

Duration: 1 day

Structure Based Design with Pharmacophores

The Structure-Based Pharmacophore (SBP) method uses the known or suspected active site of a protein to select compounds that are likely to bind within that site. The defined active site is first analyzed to create an interaction map of features that the ligand is expected to satisfy for a reasonable interaction with the protein. The feature interaction map is then used as the basis to create an input pharmacophore model.

This course covers the steps necessary to create structure based pharmacophores as well as the tools/protocols available in Discovery Studio to help with the validation and analysis of such models.

Duration: 0.75 day

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