Dataset ------- The *e*Repo-ORP repository contains data generated for the repositioning of [DrugBank][1] drugs to [Orphanet][2] proteins. The following files are included: ### Lists **`drugbank-orphanet.list`** A list of pairs of DrugBank and Orphanet proteins sorted by the [*e*MatchSite][3] score. * 1st column is the rank * 2nd column is the UniProt-ID of the DrugBank protein * 3rd column is the UniProt-ID of the Orphanet protein * 4th column is the *e*MatchSite score for Drugbank->Orphanet * 5th column is Spearman’s ρ for structure-based virtual screening with Vina * 6th column is the TM-score for Drugbank->Orphanet * 7th column is the GDT-score estimated for the *e*Thread model of the DrugBank protein * 8th column is the PDB-ID of the template used to build the *e*Thread model of the DrugBank protein * 9th column is the sequence identity between the template and the DrugBank protein * 10th column is the GDT-score estimated for the *e*Thread model of the Orphanet protein * 11th column is the PDB-ID of the template used to build the *e*Thread model of the Orphanet protein * 12th column is the sequence identity between the template and the Orphanet protein * 13th column is the confidence for the top-ranked binding site predicted by *e*FindSite in the DrugBank protein model * 14th column is the confidence for the top-ranked binding site predicted by *e*FindSite in the Orphanet protein model * 15th column is the list of DrugBank drugs separated by colons ### Data **`data-drugbank.tar.gz`** A tarball containing the following files for [DrugBank][4] targets ([Q9RVD6][5] as an example): * structure model in PDB format (`Q9RVD6.pdb`) * sequence profile by [PROFILpro 1.1][6] (`Q9RVD6.profile`) * secondary structure by [PSIPRED 4.0][7] (`Q9RVD6.ss2`) * pockets by [*e*FindSite 1.3][8] (`Q9RVD6-efindsite.pockets.dat`) * pockets by [*e*FindSite 1.3][9] in PDB format (`Q9RVD6-efindsite.pockets.pdb`) * template-target structure alignments by [*e*FindSite 1.3][10] (`Q9RVD6-efindsite.alignments.dat`) * ligands bound to templates extracted by [*e*FindSite 1.3][11] (`Q9RVD6-efindsite.ligands.sdf`) **`data-orphanet.tar.gz`** A tarball containing the following files for [Orphanet][12] targets ([P10644][13] as an example): * structure model in PDB format (`P10644.pdb`) * sequence profile by [PROFILpro 1.1][14] (`P10644.profile`) * secondary structure by [PSIPRED 4.0][15] (`P10644.ss2`) * pockets by [*e*FindSite 1.3][16] (`P10644-efindsite.pockets.dat`) * pockets by [*e*FindSite 1.3][17] in PDB format (`P10644-efindsite.pockets.pdb`) * template-target structure alignments by [*e*FindSite 1.3][18] (`P10644-efindsite.alignments.dat`) * ligands bound to templates extracted by [*e*FindSite 1.3][19] (`P10644-efindsite.ligands.sdf`) ### Complexes **`data-drugbank-complexes.tar.gz`** A tarball containing structure models of [DrugBank][20] complexes. For example, a PDB file **`P06239-DB08901.pdb`** contains the model of ponatinib ([DB08901][21]) bound to tyrosine-protein kinase Lck ([P06239][22]). The REMARK section provides several energy scores calculated for this complex with [DFIRE][23], [DSX][24], and [LPC][25]. **`data-orphanet-complexes.tar.gz`** A tarball containing complex models of [DrugBank][26] drugs repositioned to [Orphanet][27] proteins. For example, a PDB file **`Q9ULC3-DB08901-P06239.pdb`** contains the model of ponatinib ([DB08901][28]) repositioned to Ras-related protein Rab-23 ([Q9ULC3][29]) through its local alignment to tyrosine-protein kinase Lck ([P06239][30]). The REMARK section provides several energy scores calculated for this complex with [DFIRE][23], [DSX][24], and [LPC][25]. [1]: https://www.drugbank.ca/ [2]: http://www.orpha.net/ [3]: https://www.ncbi.nlm.nih.gov/pubmed/25232727 [4]: https://www.drugbank.ca/ [5]: http://www.uniprot.org/uniprot/Q9RVD6 [6]: https://www.ncbi.nlm.nih.gov/pubmed/15980571 [7]: https://www.ncbi.nlm.nih.gov/pubmed/10493868 [8]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [9]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [10]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [11]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [12]: http://www.orpha.net/ [13]: http://www.uniprot.org/uniprot/P10644 [14]: https://www.ncbi.nlm.nih.gov/pubmed/15980571 [15]: https://www.ncbi.nlm.nih.gov/pubmed/10493868 [16]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [17]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [18]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [19]: https://www.ncbi.nlm.nih.gov/pubmed/23838840 [20]: https://www.drugbank.ca/ [21]: https://www.drugbank.ca/drugs/DB08901 [22]: http://www.uniprot.org/uniprot/P06239 [23]: https://www.ncbi.nlm.nih.gov/pubmed/15801826 [24]: https://www.ncbi.nlm.nih.gov/pubmed/21863864 [25]: https://www.ncbi.nlm.nih.gov/pubmed/10320401 [26]: https://www.drugbank.ca/ [27]: http://www.orpha.net/ [28]: https://www.drugbank.ca/drugs/DB08901 [29]: http://www.uniprot.org/uniprot/Q9ULC3 [30]: http://www.uniprot.org/uniprot/P06239