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SETD8 wild-type apo and cofactor-bound, and mutant apo Folding@home simulations

Main project repository

Additional project documentation, data, and scripts can be found here:

https://github.com/choderalab/SETD8-materials

Trajectories without solvent

The following Folding@home projects were analyzed for the manuscript, and are made available here without solvent:

APO

wild type apo-SETD8

11707:

  • RUN0: 1ZKK A
  • RUN2: 1ZKK B
  • RUN3: 1ZKK D
  • RUN4: 2BQZ A
  • RUN5: 2BQZ E
  • RUN6: 3F9W A
  • RUN9: 3F9W D
  • RUN11: 3F9X C
  • RUN12: 3F9X B
  • RUN13: 3F9X D
  • RUN14: 3F9Y A
  • RUN15: 3F9Y B
  • RUN17: 3F9Z C
  • RUN18: 3F9Z B
  • RUN19: 3F9Z D
  • RUN20: 4IJ8 A
  • RUN21: 4IJ8 B
  • RUN23: 6BOZ A
  • RUN29: 6BOZ A
  • RUN36-38: 6BOZ A
  • RUN42-50: 4IJ8 A
  • RUN51-59: 4IJ8 B
  • RUN70-74: 6BOZ A
  • RUN80-99: 5V2N A
  • RUN100-109: 6BOZ B
  • RUN110: 3F9W B
  • RUN111: 3F9W C
  • RUN112: 3F9X A
  • RUN113-122: 5W1Y A
  • RUN123-132: 5W1Y B
  • RUN133: 1ZKK A
  • RUN134: 3F9Z B
  • RUN135-151: 4IJ8 A - 5W1Y A structural chimera
  • RUN152-168: 5V2N A - 5W1Y A structural chimera

11709:

  • RUN0: 1ZKK A - 5V2N A structural chimera
  • RUN1: 4IJ8 A - 5V2N A structural chimera
  • RUN2: 6BOZ A - 5V2N A structural chimera
  • RUN3: 4IJ8 A - 5V2N A structural chimera

SAM

cofactor (SAM)-bound SETD8

11710:

  • RUN0: 2BQZ A
  • RUN2: 4IJ8 A

MUTANTS

mutant apo-SETD8 modeled on 1ZKK A

11713:

  • RUN0: A237V
  • RUN1: R244S
  • RUN2: I247L
  • RUN3: E257K
  • RUN4: T274I
  • RUN5: R279Q
  • RUN6: R279W
  • RUN7: G280S
  • RUN8: V283M
  • RUN9: A296T
  • RUN10: A301V
  • RUN11: T309M
  • RUN12: C324del
  • RUN13: E330Q
  • RUN14: R333C
  • RUN15: R333L
  • RUN16: L334P
  • RUN17: H340D
  • RUN18: D325Y
  • RUN19: V356I
  • RUN20: L359F
  • RUN21: A368V
  • RUN22: E372D
  • RUN23: H388Q

Each trajectory is available in the appropriate project folder:

SETD8 <protein system> > <project number>

with trajectory files formatted as run<RUN>-clone<CLONE>.h5, with <RUN> indexing a set of trajectories started from the same conformation and <CLONE> denoting different replicates initiated from the same structure but different initial velocities.

These trajectories are stored in MDTraj HDF5 format. This is a compact, platform-portable format that contains both topology information (atom names, connectivity, and residue information) and trajectory data. You can use the freely-available MDTraj package to convert to other popular trajectory formats.

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