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# Integrative Modeling of Membrane-associated Protein Assemblies: Dataset | ||
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## 1. Introduction | ||
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This is the repository containing the dataset for the *Integrative Modeling of Membrane-associated Protein Assemblies* manuscript. | ||
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![Benchmark](media/benchmark.png) | ||
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## 2. Data organization | ||
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In top folder: | ||
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* `pdbs.list`: list of all the PDB codes of the benchmark. | ||
* `antibodies.list`: list of all the PDB codes of the benchmark which are antibody complexes (category **A** in figure). | ||
* `barrel.list`: list of all the PDB codes of the benchmark which structure is beta-barrel (category **B** in figure). | ||
* `helical.list`: list of all the PDB codes of the benchmark which structure is helical (category **C** in figure). | ||
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### 2.1. Docking | ||
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Docking protocols can be found in the `docking` folder. For each of the two protocols (LightDock and ZDock), data for the different scenarios is provided: | ||
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#### 2.1.1. LightDock | ||
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Folder `docking/lightdock` containts data for the different five scenarios: `average`, `blind`, `filtered`, `membrane` and `minimum`. | ||
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Each of the scenarios contains for the 18 complexes of the benchmark the following data: | ||
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* `lgd_clustered_rank.list`: Ranking of the top clustered structures generated by LightDock. For each line, name of the PDB complex file and values for fnat, i-RMSD, l-RMSD and LightDock score are provided. | ||
* `top100.tgz`: Top 100 predicted models generated by LightDock. | ||
* `setup.json`: LightDock generated setup file which contains information about all the parameters used for the setup of the simulation. | ||
* `receptor_membrane.pdb` or `receptor.pdb`: Starting receptor PDB structure. If file contains membrane beads, name contains the word *membrane*. | ||
* `ligand.pdb`: Starting ligand PDB structure | ||
* `lightdock_*` files: LightDock parsed and processed PDB structures. | ||
* `restraints.list`: residue restraints in the LightDock-ready format. | ||
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#### 2.1.2. ZDock | ||
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Folder `docking/zdock` containts data for the different four scenarios: `average`, `blind`, `maximum` and `minimum`. | ||
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Each of the scenarios contains for the 18 complexes of the benchmark the following data: | ||
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* `zdock_rank.list`: Ranking of the top structures generated by ZDock. For each line, name of the PDB complex file and values for fnat, i-RMSD and l-RMSD are provided. | ||
* `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). | ||
* `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). | ||
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### 2.2. Refinement | ||
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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: | ||
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* `haddock_rank.list`: for each of the diffeerent models refined, values for fnat, i-RMSD, l-RMSD and scoring is provided. For example: | ||
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``` | ||
1k4c_80w.pdb 0.0 20.182 50.751 -217.43964 | ||
``` | ||
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* `models.tgz`: compressed tar archive which contains the top 100 models refined by the HADDOCK-CG protocol. |
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