References¶
qsarkit implements no undocumented algorithms. Every class docstring cites the original publication with its DOI, and the official implementation or API documentation where it wraps one. This page collects the primary references by area; the API reference has the complete list per class.
Validation and curation¶
OECD (2007). Guidance Document on the Validation of (Quantitative) Structure-Activity Relationship [(Q)SAR] Models. OECD Series on Testing and Assessment No. 69, ENV/JM/MONO(2007)2. doi:10.1787/9789264085442-en
Golbraikh, A. & Tropsha, A. (2002). “Beware of q²!” J. Mol. Graph. Model., 20(4), 269-276. doi:10.1016/S1093-3263(01)00123-1
Consonni, V., Ballabio, D. & Todeschini, R. (2009). J. Chem. Inf. Model., 49(7), 1669-1678. doi:10.1021/ci900115y
Rücker, C., Rücker, G. & Meringer, M. (2007). J. Chem. Inf. Model., 47(6), 2345-2357. doi:10.1021/ci700157b
Gramatica, P. (2007). QSAR Comb. Sci., 26(5), 694-701. doi:10.1002/qsar.200610151
Fourches, D., Muratov, E. & Tropsha, A. (2010). J. Chem. Inf. Model., 50(7), 1189-1204. doi:10.1021/ci100176x
Sahigara, F. et al. (2012). Molecules, 17(5), 4791-4810. doi:10.3390/molecules17054791
Truchon, J.-F. & Bayly, C. I. (2007). J. Chem. Inf. Model., 47(2), 488-508. doi:10.1021/ci600426e
Representation¶
Rogers, D. & Hahn, M. (2010). J. Chem. Inf. Model., 50(5), 742-754. doi:10.1021/ci100050t
Durant, J. L. et al. (2002). J. Chem. Inf. Comput. Sci., 42(6), 1273-1280. doi:10.1021/ci010132r
Carhart, R. E., Smith, D. H. & Venkataraghavan, R. (1985). J. Chem. Inf. Comput. Sci., 25(2), 64-73. doi:10.1021/ci00046a002
Bajusz, D., Rácz, A. & Héberger, K. (2015). J. Cheminform., 7, 20. doi:10.1186/s13321-015-0069-3
Jaeger, S., Fulle, S. & Turk, S. (2018). J. Chem. Inf. Model., 58(1), 27-35. doi:10.1021/acs.jcim.7b00616
Chithrananda, S., Grand, G. & Ramsundar, B. (2020). arXiv:2010.09885
Gilmer, J. et al. (2017). arXiv:1704.01212
Yang, K. et al. (2019). J. Chem. Inf. Model., 59(8), 3370-3388. doi:10.1021/acs.jcim.9b00237
Kipf, T. N. & Welling, M. (2017). arXiv:1609.02907
Veličković, P. et al. (2018). arXiv:1710.10903
Schütt, K. T. et al. (2018). J. Chem. Phys., 148, 241722. doi:10.1063/1.5019779
Riniker, S. & Landrum, G. A. (2015). J. Chem. Inf. Model., 55(12), 2562-2574. doi:10.1021/acs.jcim.5b00654
SAR analysis¶
Maggiora, G. M. (2006). J. Chem. Inf. Model., 46(4), 1535. doi:10.1021/ci060117s
Guha, R. & Van Drie, J. H. (2008). J. Chem. Inf. Model., 48(3), 646-658. doi:10.1021/ci7004093
Hussain, J. & Rea, C. (2010). J. Chem. Inf. Model., 50(3), 339-348. doi:10.1021/ci900450m
Stumpfe, D. & Bajorath, J. (2012). J. Med. Chem., 55(7), 2932-2942. doi:10.1021/jm300288g
Peltason, L. & Bajorath, J. (2007). J. Med. Chem., 50(23), 5571-5578. doi:10.1021/jm070562u
Free, S. M. & Wilson, J. W. (1964). J. Med. Chem., 7(4), 395-399. doi:10.1021/jm00334a001
van Tilborg, D., Alenicheva, A. & Grisoni, F. (2022). J. Chem. Inf. Model., 62(23), 5938-5951. doi:10.1021/acs.jcim.2c01073
Clustering and diversity¶
Butina, D. (1999). J. Chem. Inf. Comput. Sci., 39(4), 747-750. doi:10.1021/ci9803381
Taylor, R. (1995). J. Chem. Inf. Comput. Sci., 35(1), 59-67. doi:10.1021/ci00023a009
Ashton, M. et al. (2002). Quant. Struct.-Act. Relat., 21(6), 598-604. doi:10.1002/qsar.200290002
Willett, P., Barnard, J. M. & Downs, G. M. (1998). J. Chem. Inf. Comput. Sci., 38(6), 983-996. doi:10.1021/ci9800211
Docking and structure-based modeling¶
Trott, O. & Olson, A. J. (2010). J. Comput. Chem., 31(2), 455-461. doi:10.1002/jcc.21334
Eberhardt, J. et al. (2021). J. Chem. Inf. Model., 61(8), 3891-3898. doi:10.1021/acs.jcim.1c00203
Salentin, S. et al. (2015). Nucleic Acids Res., 43(W1), W443-W447. doi:10.1093/nar/gkv315
Le Guilloux, V., Schmidtke, P. & Tuffery, P. (2009). BMC Bioinformatics, 10, 168. doi:10.1186/1471-2105-10-168
Krivák, R. & Hoksza, D. (2018). J. Cheminform., 10, 39. doi:10.1186/s13321-018-0285-8
Ballester, P. J. & Mitchell, J. B. O. (2010). Bioinformatics, 26(9), 1169-1175. doi:10.1093/bioinformatics/btq112
Deng, Z., Chuaqui, C. & Singh, J. (2004). J. Med. Chem., 47(2), 337-344. doi:10.1021/jm030331x
Shrake, A. & Rupley, J. A. (1973). J. Mol. Biol., 79(2), 351-371. doi:10.1016/0022-2836(73)90011-9
Design and optimization¶
Bemis, G. W. & Murcko, M. A. (1996). J. Med. Chem., 39(15), 2887-2893. doi:10.1021/jm9602928
Meanwell, N. A. (2011). J. Med. Chem., 54(8), 2529-2591. doi:10.1021/jm1013693
Deb, K. et al. (2002). IEEE Trans. Evol. Comput., 6(2), 182-197. doi:10.1109/4235.996017
Jensen, J. H. (2019). Chem. Sci., 10, 3567-3572. doi:10.1039/C8SC05372C
Ertl, P. & Schuffenhauer, A. (2009). J. Cheminform., 1, 8. doi:10.1186/1758-2946-1-8
Hartenfeller, M. et al. (2011). J. Chem. Inf. Model., 51(12), 3093-3098. doi:10.1021/ci200379p
ADMET¶
Lipinski, C. A. et al. (2001). Adv. Drug Deliv. Rev., 46(1-3), 3-26. doi:10.1016/S0169-409X(96)00423-1
Veber, D. F. et al. (2002). J. Med. Chem., 45(12), 2615-2623. doi:10.1021/jm020017n
Bickerton, G. R. et al. (2012). Nat. Chem., 4, 90-98. doi:10.1038/nchem.1243
Baell, J. B. & Holloway, G. A. (2010). J. Med. Chem., 53(7), 2719-2740. doi:10.1021/jm901137j
Delaney, J. S. (2004). J. Chem. Inf. Comput. Sci., 44(3), 1000-1005. doi:10.1021/ci034243x
Daina, A. & Zoete, V. (2016). ChemMedChem, 11(11), 1117-1121. doi:10.1002/cmdc.201600182
Databases¶
Kim, S. et al. (2023). “PubChem 2023 Update.” Nucleic Acids Res., 51(D1), D1373-D1380. doi:10.1093/nar/gkac956
Zdrazil, B. et al. (2024). “The ChEMBL Database in 2023.” Nucleic Acids Res., 52(D1), D1180-D1192. doi:10.1093/nar/gkad1004
Irwin, J. J. et al. (2020). “ZINC20.” J. Chem. Inf. Model., 60(12), 6065-6073. doi:10.1021/acs.jcim.0c00675
Burley, S. K. et al. (2023). “RCSB Protein Data Bank.” Nucleic Acids Res., 51(D1), D488-D508. doi:10.1093/nar/gkac1077
Knox, C. et al. (2024). “DrugBank 6.0.” Nucleic Acids Res., 52(D1), D1265-D1275. doi:10.1093/nar/gkad976
Software¶
RDKit: Open-source cheminformatics. https://www.rdkit.org
Pedregosa, F. et al. (2011). “Scikit-learn.” J. Mach. Learn. Res., 12, 2825-2830. https://jmlr.org/papers/v12/pedregosa11a.html
Harris, C. R. et al. (2020). “Array Programming with NumPy.” Nature, 585, 357-362. doi:10.1038/s41586-020-2649-2
Hagberg, A., Schult, D. & Swart, P. (2008). “Exploring Network Structure with NetworkX.” Proc. SciPy 2008.