Dataset ------- **TOUGH-D1** comprises the experimental structures of ligand-protein complexes having aromatic contacts at the interface. The following files are included: ### Lists **`TOUGH-D1_complex.list`** A list of 3079 complexes ### Data **`TOUGH-D1_dataset.tar.gz`** A tarball containing the following files ([13pkD][1] as an example): * target structure in PDB format (`13pkD.pdb`) * bound ligand in MOL format (`13pkD.mol`) * ligand-protein contacts by [LPC][2] (`13pkD.lpc`) * aromatic contacts by *e*Aromatic (`13pkD.aromatic`) Please refer to the documentation of *e*Aromatic available at [https://github.com/michal-brylinski/earomatic][3] for the description of the output file format. Results ------- Output files generated for the TOUGH-D1 dataset by ligand docking algorithms are available to facilitate comparative benchmarks. These files are in the SDF format and include the following scores: * `RMSD`: root-mean-square deviation from the experimental structure calculated over non-hydrogen ligand atoms * `CMS`: [Contact Mode Score][4] calculated against the experimental complex structure * `DSX_SCORE`: energy score reported by [DSX][5] * `LPC_SCORE`: complementarity score reported by [LPC][6] * `DFIRE_SCORE`: energy score reported by [DFIRE][7] * `VINA_SCORE`: energy score reported by [AutoDock Vina][10] * `RDOCK_SCORE`: energy score reported by [rDock][12] The following conformations are included: ### Reference conformations **`native-like-TOUGH-D1.tar.gz`** Native-like configurations having a [CMS][8] of ≥0.5 **`random-TOUGH-D1.tar.gz`** Random configurations having a [CMS][9] of <0.3 ### Molecular docking **`Vina-TOUGH-D1.tar.gz`** High-scoring models reported by [AutoDock Vina][11] **`rDock-TOUGH-D1.tar.gz`** High-scoring models reported by [rDock][12] [1]: http://www.rcsb.org/pdb/explore.do?structureId=13pk [2]: https://www.ncbi.nlm.nih.gov/pubmed/10320401 [3]: https://github.com/michal-brylinski/earomatic [4]: https://www.ncbi.nlm.nih.gov/pubmed/27620381 [5]: https://www.ncbi.nlm.nih.gov/pubmed/21863864 [6]: https://www.ncbi.nlm.nih.gov/pubmed/10320401 [7]: https://www.ncbi.nlm.nih.gov/pubmed/15801826 [8]: https://www.ncbi.nlm.nih.gov/pubmed/27620381 [9]: https://www.ncbi.nlm.nih.gov/pubmed/27620381 [10]: https://www.ncbi.nlm.nih.gov/pubmed/19499576 [11]: https://www.ncbi.nlm.nih.gov/pubmed/19499576 [12]: https://www.ncbi.nlm.nih.gov/pubmed/24722481