1. AlphaFold2

1-1. MSA Data
Format: Pickle format
Contents: Multiple Sequence Alignment (MSA) data.

1-2. MSA Coverage
Information on the coverage of sequences in the MSA.

1-3. Predicted Alignment Error
Prediction of errors in the alignment.

1-4. Predicted Contacts
Predicted residue-residue contacts, showing which residues are predicted to be close in the 3D structure.

1-5. Predicted Distogram
A distance histogram, indicating predicted distances between pairs of residues.

1-6. Predicted Local Distance Difference Test (LDDT)
A quality measure of the predicted structure, evaluating the local distance between atoms in the predicted structure and a reference structure.

1-7. Structures (Rank 1 to Rank 5)
Raw Data: Structures corresponding to the top 5 prediction ranks.
PAE Data: Prediction Accuracy Estimation (PAE) data in JSON format.
Unrelaxed Structure: The unrelaxed version of the predicted structure in PDB format, which is the initial structure before any energy minimization or relaxation steps.

1-8. Settings
Configuration settings used during the prediction process, such as hyperparameters, model parameters, etc.

2. Molecular Dynamics

2-1. Forcefield
CHARMM36m (March 2019)

2-2. Solvated Structures
Solvated structure in PDB format, containing the molecular structure with water and ions added for simulations.

2-3. ions.mdp
Input and parameter file for generating iont.tpr file.

2-4. em.mdp
Input and parameter file for energy minimization.

2-5. nvt.mdp
Input and parameter file for NVT simulation.

2-6. npt.mdp
Input and parameter file for NPT simulation.

2-7. md.mdp
Input and parameter file for production MD simulation.

2-8. topol.top
Topology file for the system.

2-9. topol_Protein_chain_A.itp
Topology file for the SH3 system.

2-10. topol_Protein_chain_B.itp
Topology file for the PRM or PRM(H) series.

2-11. posre_Protein_chain_A.itp
Auxiliary topology file for restraining the SH3 system.

2-12. posre_Protein_chain_B.itp
Auxiliary topology file for restraining the PRM or PRM(H) series.

Contact: sejunkim@caltech.edu