Molecular Visualization & Bioinformatics

Background Information

• HawkDock Website

• Student PyMOL Site

• PyMOL Wiki

• Paper on GalaxyRefine

Protocols

• Exploring Titratable Groups H++

• Identifying Binding Sites

Seam Dock Tutorial (a simple way to dock a ligand to a PDB file

• Tutorial

• Reference Paper

Two introduction tutorials on Alpha Fold 3 - Use to fold protein, predict interactions and estimate impact of mutation and PTM. The second is how to analyze. The is a first video to give a quick method to use the new computational tool. Suggestions or problems? Email Chris Berndsen berndsce@jmu.edu

• Using Alpha Fold 3 (including PTM)

• Analyzing Alpha Fold 3 Results

Tutorials/ Videos

• PyMOL Tutorials (Creating Movie Scenes) (Movies with Morphing) (Aligning Structures) (Mutate Structures)

• Molecular Memory PyMOL Tutorials (Active Site) (Working with Scenes) (Labels) (Protein Interactions) (Dimers)

• MCC Workshop on Computational CURES

• Swanson PyMol Tutorials (PyMol for Beginners), (Labels), (Measurements), (Hydrogen Bonds), (Alignment), (Mutagenesis)

• GalaxyRefine (Website), (Tutorial)

Teaching Files

• Biochem Lab Worksheet Handout

• MCC PyMOL Homework

STRUCTURES

hMDH2 key sites (PSE)

AMY Chimera Test

hMDH1 all phospho (PSE)

4kde_6ihe_aligned Loop shift (PSE)