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brianjimenez committed Jun 18, 2020
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Expand Up @@ -44,20 +44,20 @@ Each of the scenarios contains for the 18 complexes of the benchmark the followi
* `zdock.out`: Result of the ZDock simulation.
* `top100.tgz`: Top 100 predicted models generated by ZDock.
* `receptor.pdb` and `ligand.pdb`: PDB files for the starting structures (receptor and ligand respectively).
* `*.block`: list of residued blocked for the scenario. In case of antibody-antigen complex, a `cdr.block` file is also provided with the list of blocked residues corresponding to the CDR predicted loops.
* `receptor_rotated.pdb` and `ligand_rotated.pdb`: PDB files for the starting structures after being randomly rotated to avoid simulation artifcats (receptor and ligand respectively).
* `*.block`: list of residues blocked for the scenario. In case of antibody-antigen complex, a `cdr.block` file is also provided with the list of blocked residues corresponding to the CDR predicted loops.
* `receptor_rotated.pdb` and `ligand_rotated.pdb`: PDB files for the starting structures after being randomly rotated to avoid simulation artifacts (receptor and ligand respectively).
* `receptor_blocked.pdb` and `ligand_blocked.pdb`: PDB files with blocked residues according to the ZDock protocol (receptor and ligand respectively).
* `receptor_surface.pdb` and `ligand_surface.pdb`: PDB files with marked surface residues according to the ZDock protocol (receptor and ligand respectively).


### 2.2. Refinement

Refinement with HADDOCK-CG protocol can be found at `refinement/haddock`. Results of the refinment protocol for two scenarios are provided: `blind` and `membrane`. Each of those scenarios contains a folder for each of the complexes of the dataset. For each complex, two files are provided:
Refinement with HADDOCK-CG protocol can be found at `refinement/haddock`. Results of the refinement protocol for two scenarios are provided: `blind` and `membrane`. Each of these scenarios contains a folder for each of the complexes of the dataset. For each complex, two files are provided:

* `haddock_rank.list`: for each of the diffeerent models refined, values for fnat, i-RMSD, l-RMSD and scoring is provided. For example:

```
1k4c_80w.pdb 0.0 20.182 50.751 -217.43964
```

* `models.tgz`: compressed tar archive which contains the top 100 models refined by the HADDOCK-CG protocol.
* `models.tgz`: compressed tar archive which contains the top 100 models refined by the HADDOCK-CG protocol.

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