AlphaSpace2_Tutorials

The following tutorials were made for the AlphaSpace2 platform. The tutorials below show how AlphaSpace2 and Beta Clusters can be used for a wide variety of applications in drug discovery, from binding site detection, comparison, and design. To use these tutorials, install AlphaSpace2 and run these jupyter notebooks. The necessary pdb and ligan structures are located in the folders corresponding to each tutorial.

• Calculating Beta Cluster Features
• Scripts to Compare Binding Sites between different proteins
• NMR Ensemble comparison of the MDM2/MDM4 Binding Sites
• Pocket Community Detection for CDK2
• Pocket Guided Fragment Based Design