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Small Molecule Drug Discovery

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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+.
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A Chemist's Guide to Maestro
Basic Maestro tasks useful for medicinal chemists during idea generation and lead optimization.
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Using IFD-MD on a Membrane-bound protein
Set up a membrane-bound protein for IFD-MD and visualize the results.
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Training and Evaluating ADMET Models with DeepAutoQSAR
Build and test two models for predicting aqueous solubility using a large dataset
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Forming Protein-Ligand Interactions with the Ligand Designer
Form protein-ligand interactions and optimize a hit molecule with the Ligand Designer.
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WaterMap-Guided Lead Optimization with the Ligand Designer
Displace an unstable water an optimize a hit molecule with the Ligand Designer.
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Batch Homology Modeling Using the Multiple Sequence Viewer/Editor
Build multiple homology models using a single template with the MSV.
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Building Homology Models with the Multiple Sequence Viewer/Editor
Build and refine a homology model with the MSV.
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Enumeration Tools for Library Design
Use enumeration tools to design libraries for lead optimization of a CDK2 inhibitor
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Introduction to Structure Preparation and Visualization
Preparation and visualization of ligand and protein structures in Maestro.
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Locating Transition States: Part 1
Locate a transition state (TS) for a typical organometallic reaction via three methods: standard TS search, coordinate...
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Introduction to Geometry Optimizations, Functionals and Basis Sets
Perform geometry optimizations on simple organic molecules and learn basics regarding functionals and basis sets.
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Using IFD-MD on a Covalently Bound Ligand
Set up IFD-MD for a covalently bound ligand and visualize the results.
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Heteromultimer Homology Modeling with the Multiple Sequence Viewer/Editor
Build a heteromultimer homology model of human hemoglobin from a bar-head goose hemoglobin structure.
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Membrane-Bound FEP+ with A2A
Prepare, run, and analyze a free energy perturbation (FEP) simulation with a membrane-bound protein for a series of A2A...
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Evaluating Large Ligand Libraries with Active Learning Glide
Set up a virtual screen to analyze a 1M ligand library from using Active Learning Glide.
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Chimeric Homology Modeling Using the Multiple Sequence Viewer/Editor
Build a chimeric homology model using the Multiple Sequence Viewer/Editor (MSV).
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Rapid Screening of Chemical Libraries with GPU Shape
Perform rapid shape-based screening of a 20,000 compound chemical library with GPU Shape.
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Identifying Binding Site Requirements and Lead Optimization with WaterMap
Examine results from WaterMap and WM/MM scoring to identify unstable waters and evaluate ligand binding.
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Target Analysis with SiteMap and WaterMap
Identify potential active sites on a receptor
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Conformational Analysis for Small Molecules Using MacroModel and ConfGen
Investigate torsional profiles for related small molecules and how conformation affects intra- and intermolecular...
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Structure-Based Lead Optimization with Glide and MM-GBSA
Optimize binding poses, investigate core constraints, and rank-order a congeneric series of inhibitors
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Structure-Based Virtual Screening using Glide
Prepare receptor grids for docking, dock molecules and examine the docked poses
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Locating Transition States: Part 2
Demonstrate how to use a known transition state to locate the transition state of a similar reaction.
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