Training
Small Molecule Drug Discovery
BACE1 Inhibitor Design Using Free Energy Perturbation
Prepare, run, and analyze a free energy perturbation (FEP) simulation for a series of BACE1 inhibitors using FEP+.
WaterMap-Guided Lead Optimization with the Ligand Designer
Examine results from WaterMap and WM/MM scoring to identify unstable waters and evaluate ligand binding.
WScore Evaulation of HSP90 Ligands
Build and use WScore models to evaluate Hsp90 ligands.
Structure-Based Virtual Screening Using Phase Workshop Tutorial
Create and analyze pharmacophore models generated from a protein-ligand complex.
Target Analysis with SiteMap and WaterMap
Identify potential active sites on a receptor
Structure-Based Virtual Screening Using Glide Workshop Tutorial
Prepare receptor grids for docking, dock molecules and examine the docked poses.
Structure-Based Lead Optimization with Glide & MM-GBSA
Optimize binding poses, investigate core constraints, and rank-order a congeneric series of inhibitors
Small Molecule Membrane Permeability Workshop Tutorial
Predict the membrane permeability of a series of small molecules.
Rapid Screening of Chemical Libraries with GPU Shape
Perform rapid shape-based screening of a 20,000 compound chemical library with GPU Shape.
pKa Predictions with Jaguar pKa Workshop Tutorial
Predict the pKa of organic molecules with more than one acidic functional group.
Ligand-Based Virtual Screening Using Phase Workshop Tutorial
Create and analyze pharmacophore hypotheses from congeneric and diverse ligand sets
Introduction to Structure Visualization and Preparation Workshop Tutorial
Preparation and visualization of ligand and protein structures in Maestro.
Library Design: Enumeration Tools
Use enumeration tools to design libraries for lead optimization of a CDK2 inhibitor.
Identifying Binding Site Requirements and Hit-to-Lead with WaterMap
Examine results from WaterMap and WM/MM scoring to identify unstable waters and evaluate ligand binding.
Forming Protein-Ligand Interactions with the Ligand Designer
Form protein-ligand interactions and optimize a hit molecule with the Ligand Designer.
Homology Modeling of Protein-Ligand Binding Sites with IFD-MD
Create a homology model of TYK2, including a bound ligand, using the structure of JAK3 as a starting point. Then you...
Drug Development with Macrocycles Workshop Tutorial
Sampling, docking, and lead optimization of macrocycles.
Evaluating Large Ligand Libraries with Active Learning Glide
Set up a virtual screen to analyze a 1M ligand library from using Active Learning Glide.
Cross-docking with IFD-MD
Using IFD-MD to generate a predicted binding pose of a known active compound using a holo crystal structure solved with...
Defining QM and MM Regions in QSite
Define regions to treat with QM and with MM for a QSite calculation.
Conformational Analysis for Small Molecules using Macromodel/ConfGen
Investigate torsional profiles for related small molecules and how conformation affects intra- and intermolecular...
Covalent Docking for Pose Prediction
Dock a set of ligands that bind covalently to the receptor, using predefined or custom reaction chemistry.
Building QSAR Models with AutoQSAR/DeepChem Workshop Tutorial
Create, interpret, and apply deep-learning QSAR models using DeepChem.
A Chemist’s Guide to Maestro Workshop Tutorial
Basic Maestro tasks useful for medicinal chemists during idea generation and lead optimization.