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ccp5-summer-school's Introduction

CCP5 Summer School 2022

Links

Installing PyMol.

Register PyMol with an Educational License

Practical 1: AlphaFold

Links to the online AlphaFold implementations

BRAF FASTA sequence:

KTLGRDSDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQLQAFKNEVGVLRKTRHVNILFMGYSTKPQLAIVTQWCEGSLYHLHIETKFEMIKLIDIARQTAQGMDYLHAKSIHRDLKSNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINRDQIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKRDERPLFPQILASIELARSLPKIKIRPRGQRDSYWEIE

AlphaFold Database

Practical 2: CDK2-Ligand Complex Simulation

Important files are in the screening-docking folder and the CHARMM-GUI folder

Link to the docking/screening software, DockBlaster

The Zinc Database

Our ligand on the database

CHARMM-GUI

Practical 3: GPI-CD59 in plasma membrane

CD59 PDB structure

Membrane Lipids:

Leaflet Cholesterol POPE PSM
upper leaflet 72 74 67
lower leaflet 73 75 68

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