Benchmarking dataset ------- **`clusters.yaml`**: binding site clusters **`protein-data`**: protein features: * `*.fasta` protein sequence in the [FASTA][1] format * `*.pdb` protein structure in the [PDB][2] format * `*.pops` protein surface calculated by the [POPS][3] program * `*.profile` protein sequence profile calculated by the [PROFILpro][4] program **`pocket-data`**: pocket features: * `*.lpc` ligand-protein contacts calculated by the [LPC][5] program * `*.mol2` pocket structure in the [mol2][6] format * `*.pdb` pocket structure in the [PDB][2] format * `*.sdf` binding ligand in the [SDF][7] format Unseen dataset ------- **`unseen_data_results.txt`**: prediction results for unseen data **`unseen-data`**: * `*.fasta` protein sequence in the [FASTA][1] format * `*.pdb` protein structure in the [PDB][2] format * `*.pops` protein surface calculated by the [POPS][3] program * `*.profile` protein sequence profile calculated by the [PROFILpro][4] program * `*.mol2` pocket structure in the [mol2][6] format Negative dataset ------- **`negative_pocket_list.txt`**: list of non-binding pockets **`negative-data`**: * `*.pops` protein surface calculated by the [POPS][3] program * `*.profile` protein sequence profile calculated by the [PROFILpro][4] program * `*.mol2` pocket structure in the [mol2][6] format **`negative_data_output_probs.yaml`**: output class probabilities for the negative dataset [1]: https://en.wikipedia.org/wiki/FASTA_format [2]: https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format) [3]: https://pubmed.ncbi.nlm.nih.gov/12824328/ [4]: http://download.igb.uci.edu/ [5]: https://pubmed.ncbi.nlm.nih.gov/10320401/ [6]: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf [7]: https://en.wikipedia.org/wiki/Chemical_table_file