Phase I: Preperation for JNK1, PTP1b, EGFR and Factor Xa

[RiesBen]

Input submission checklist

• [x] created a directory for each system based on the template directory
• [x] named and placed the directory with the following pattern: input_structures/prepared_structures/<set_name>/<system_name>

For each submitted directory:

• [x] filled in system preparation details in the PREPARATION_DETAILS.md file
• [x] added a PDB file with the protein named protein.pdb
• [x] removed any cofactors from the PDB file and placed them in cofactors.sdf
• [x] kept cystallographic waters and metals in the PDB file
• [x] tested the PDB and, if available, cofactors.sdf file using the input validation script
• [x] copied over the ligands SDF file to a file named ligands.sdf and removed any duplicate binding modes or protonation states, keeping the more favorable state

Summary of changes

Licensing agreement

• [x] I agree to release these inputs under the combined MIT and CCBY SA 4.0 licenses of this repository

[hannahbaumann]

@RiesBen : Thank you for preparing the systems! I noticed that for some systems (e.g. ptp1b) the protonation state of some side chains changed, compared to the structures by Ross et al. Is there an option to prepare the systems while not changing the protonation states but keeping the one from the original structure? For the systems that involve net charge changes we would like to simulate only a single protonation state per ligand and remove the other protonation state from the input sdf. We would like to keep the protonation state that was used in the old study (doi:10.1021/ja512751q). Could you remove the other protonation state from the inputs?

[RiesBen]

@hannahbaumann : oh will look into the protonations, thanks for pointing it out! :)

• [x] Reducing Charge Molecules to paper
• [x] Keep protonation states of protein constant - followed JoeBlucks approach