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Small Molecule Drug Discovery

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Locating Transition States: Part 1
Locate a transition state for a typical organometallic reaction via three methods: standard TS search, coordinate scan...
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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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Computing Atomic Charges with Jaguar
Calculate atomic partial charges and compare different methods for determining charges.
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Vibrational Circular Dichroism (VCD)
Learn to perform vibrational circular dichroism (VCD) calculations.
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Rigid and Relaxed Coordinate Scans
Explore potential energy surfaces using rigid and relaxed coordinate scans.
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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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Batch Homology Modeling Using the Multiple Sequence Viewer/Editor
Build multiple homology models using a single template with the MSV.
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Training and Evaluating ADMET Models with DeepChem/AutoQSAR
Build and test two models for predicting aqueous solubility using a large dataset
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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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pKa Predictions with Jaguar pKa
Predict the pKa of organic molecules with more than one acidic functional group.
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Defining QM and MM regions in QSite
Define regions to treat with QM and with MM for a QSite calculation.
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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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Obtaining Protein Free Energy Perturbation Thermostability Predictions for Single Point Mutations
Prepare, run and analyze a protein Free Energy Pertubation (FEP) simulation to obtain thermostability predictions for...
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WScore Evaluation of HSP90 Ligands
Build and use WScore models to evaluate Hsp90 ligands.
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Absolute Binding Free Energy Perturbation to Postprocess Docking Results
Use Absolute Binding Free Energy calculations to enrich virtual screening results.
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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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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...
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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...
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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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Covalent Docking for Virtual Screening and Pose Prediction
Dock a set of ligands that bind covalently to the receptor, using predefined or custom reaction chemistry.
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Small Molecule Membrane Permeability
Predict the membrane permeability of a series of small molecules.
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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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