PELIKAN Datasets

Precompiled PELIKAN databases with protein-ligand complexes of different datasets can be downloaded below. Please note that these are large binary files in a proprietary database format for use with the PELIKAN software:

sc-PDB (version 2013, obtained from http://cheminfo.u-strasbg.fr/scPDB/, approx. 12 GB) [1]

Complete PDB (accessed November 2016, obtained from www.rcsb.org, approx. 85 GB) [2]

Protein kinases (protein kinase structures obtained from http://klifs.vu-compmedchem.nl, approx. 5.5 GB) [3]

G protein-coupled receptors (structures of GPCRs obtained from http://gpcrdb.org, approx. 210 MB) [4]

PDBbind version 2014, general set (obtained from http://www.pdbbind-cn.org/, approx. 11.5 GB) [5]

PDBbind version 2014, refined set (obtained from http://www.pdbbind-cn.org/, approx. 3.5 GB) [5]

PDBbind version 2014, core set (obtained from http://www.pdbbind-cn.org/, approx. 285 MB) [5]

HIV targets (structures of reverse transcriptase, protease, and integrase structures obtained from https://hivdb.stanford.edu/pages/3DStructures/, approx. 593 MB) [6]

[1] Kellenberger, E.; Muller, P.; Schalon, C.; Bret, G.; Foata, N.; Rognan, D. sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model 2006, 46 (2), 717-727. DOI: https://doi.org/10.1021/ci050372x
[2] Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res 2000, 28 (1), 235-242. DOI: https://doi.org/10.1093/nar/28.1.235
[3] Kooistra, A. J.; Kanev, G. K.; van Linden, O. P.; Leurs, R.; de Esch, I. J.; de Graaf, C. KLIFS: a structural kinase-ligand interaction database. Nucleic Acids Res 2016, 44 (D1), D365-371. DOI: https://doi.org/10.1093/nar/gkv1082
[4] Isberg, V.; Mordalski, S.; Munk, C.; Rataj, K.; Harpsoe, K.; Hauser, A. S.; Vroling, B.; Bojarski, A. J.; Vriend, G.; Gloriam, D. E. GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res 2016, 44 (D1), D356-364. DOI: https://doi.org/10.1093/nar/gkv1178
[5] Liu, Z.; Li, Y.; Han, L.; Li, J.; Liu, J.; Zhao, Z.; Nie, W.; Liu, Y.; Wang, R. PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics 2015, 31 (3), 405-412. DOI: https://doi.org/10.1093/bioinformatics/btu626
[6] Rhee, S. Y.; Gonzales, M. J.; Kantor, R.; Betts, B. J.; Ravela, J.; Shafer, R. W. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 2003, 31 (1), 298-303. DOI: https://doi.org/10.1093/nar/gkg100