2020 DOCK tutorial 4 with PDBID XXXX

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This tutorial is created by AMS 536 Spring 2020 Group 4. Group 4 members include Steven Pak, Caitlyn Cardetti, MiaoMiao He and Chuanzhou (Joey) Hu.

How to for selecting protein: Pick a protein with few substrates and rotational bonds?

The PDB code chosen is 6UZW which is for the crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and UBP791.

Dock Prep Program used: Chimera Step 1. Delete H2O molecules in Chimera to reduce computing time. How to delete: Select > Residues > H O H - they should be highlighted Click Actions > Atoms/Bonds > delete H2O molecules should now be deleted.

PDB codes do not contain H's due to low electron density. To add H's Tools > Structure Editing > AddH

Add charges Tools > Structure Editing > Add charge Typically use AM1-BCC

Want to be careful about selecting charge because this will affect predictions for interactions (i.e. Coulomb's Law) Read paper to look at the protonation stages