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+# Integrative Modeling of Membrane-associated Protein Assemblies: Dataset
+
+## 1. Introduction
+
+This is the repository containing the dataset for the *Integrative Modeling of Membrane-associated Protein Assemblies* manuscript.
+
+![Benchmark](media/benchmark.png)
+
+
+## 2. Data organization
+
+In top folder:
+
+* `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).
+
+### 2.1. Docking
+
+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:
+
+#### 2.1.1. LightDock
+
+Folder `docking/lightdock` containts data for the different five scenarios: `average`, `blind`, `filtered`, `membrane` and `minimum`.
+
+Each of the scenarios contains for the 18 complexes of the benchmark the following data:
+
+* `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.
+
+#### 2.1.2. ZDock
+
+Folder `docking/zdock` containts data for the different four scenarios: `average`, `blind`, `maximum` and `minimum`.
+
+Each of the scenarios contains for the 18 complexes of the benchmark the following data:
+
+* `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).
+
+
+### 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:
+
+* `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.
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