Chemical database (English Wikipedia)

Harris, JB (2019). "Post-processing of Large Bioactivity Data". Bioinformatics and Drug Discovery. Methods Mol Biol. Vol. 1939. pp. 37–47. doi:10.1007/978-1-4939-9089-4_3. ISBN 978-1-4939-9088-7. PMID 30848455. S2CID 73493315.
Wang, Y; Bryant, SH; Cheng, T; Wang, J; Gindulyte, A; Shoemaker, BA; Thiessen, PA; He, S; Zhang, J (2017). "PubChem BioAssay: 2017 update". Nucleic Acids Res. 45 (D1): D955 – D963. doi:10.1093/nar/gkw1118. PMC 5210581. PMID 27899599.
Hoffmann, Torsten; Gastreich, Marcus (2019). "The next level in chemical space navigation: going far beyond enumerable compound libraries". Drug Discovery Today. 24 (5): 1148–1156. doi:10.1016/j.drudis.2019.02.013. PMID 30851414.
Sadybekov, Anastasiia V.; Katritch, Vsevolod (2023). "Computational approaches streamlining drug discovery". Nature. 616 (7958): 673–685. Bibcode:2023Natur.616..673S. doi:10.1038/s41586-023-05905-z. PMID 37100941.
Currano, Judith N. (2014). "Chapter 5. Searching by Structure and Substructure". Chemical Information for Chemists. pp. 109–145. doi:10.1039/9781782620655-00109. ISBN 978-1-84973-551-3.
Ullmann, J. R. (1976). "An Algorithm for Subgraph Isomorphism". Journal of the ACM. 23: 31–42. doi:10.1145/321921.321925.
Warr, Wendy A. (2011). "Representation of chemical structures". WIREs Computational Molecular Science. 1 (4): 557–579. doi:10.1002/wcms.36.
Pearlman, R.S.; Smith, K.M. (1999). "Metric Validation and the Receptor-Relevant Subspace Concept". J. Chem. Inf. Comput. Sci. 39: 28–35. doi:10.1021/ci980137x.
Burden, Frank R. (1 August 1989). "Molecular identification number for substructure searches". Journal of Chemical Information and Computer Sciences. 29 (3): 225–227. doi:10.1021/ci00063a011.
Pearlman, R.S.; Smith, K.M. (1999). "Metric Validation and the Receptor-Relevant Subspace Concept". J. Chem. Inf. Comput. Sci. 39: 28–35. doi:10.1021/ci980137x.
Lin, Jr., Hung; Clark, Timothy (2005). "An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties". Journal of Chemical Information and Modeling. 45 (4): 1010–1016. doi:10.1021/ci050059v. PMID 16045295.
Meek, P. J.; Liu, Z.; Tian, L.; Wang, C. J; Welsh, W. J; Zauhar, R. J (2006). "Shape Signatures: speeding up computer aided drug discovery". DDT 2006. 19–20 (19–20): 895–904. doi:10.1016/j.drudis.2006.08.014. PMID 16997139.
Grant, J. A; Gallardo, M. A.; Pickup, B. T. (1996). "A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape". Journal of Computational Chemistry. 17 (14): 1653–1666. doi:10.1002/(sici)1096-987x(19961115)17:14<1653::aid-jcc7>3.0.co;2-k. S2CID 96794688.
Ballester, P. J.; Richards, W. G. (2007). "Ultrafast shape recognition for similarity search in molecular databases". Proceedings of the Royal Society A. 463 (2081): 1307–1321. Bibcode:2007RSPSA.463.1307B. doi:10.1098/rspa.2007.1823. S2CID 12540483.
Kim, Sunghwan (2021). "Exploring Chemical Information in PubChem". Current Protocols. 1 (8): e217. doi:10.1002/cpz1.217. PMC 8363119. PMID 34370395.
Williams, Antony J. (2010). "ChemSpider: Integrating Structure-Based Resources Distributed across the Internet". Enhancing Learning with Online Resources, Social Networking, and Digital Libraries. ACS Symposium Series. Vol. 1060. pp. 23–39. doi:10.1021/bk-2010-1060.ch002. ISBN 978-0-8412-2600-5.
Jarabak, Charlotte; Mutton, Troy; Ridley, Damon D. (2020). "Property Information in Substance Records in Major Web-Based Chemical Information and Data Retrieval Tools: Understanding Content, Search Opportunities, and Application to Teaching". Journal of Chemical Education. 97 (5): 1345–1359. Bibcode:2020JChEd..97.1345J. doi:10.1021/acs.jchemed.9b00966.
Ertl, Peter; Patiny, Luc; Sander, Thomas; et al. (2015). "Wikipedia Chemical Structure Explorer: Substructure and similarity searching of molecules from Wikipedia". Journal of Cheminformatics. 7: 10. doi:10.1186/s13321-015-0061-y. PMC 4374119. PMID 25815062.
Tingle, Benjamin I.; Tang, Khanh G.; Castanon, Mar; Gutierrez, John J.; Khurelbaatar, Munkhzul; Dandarchuluun, Chinzorig; Moroz, Yurii S.; Irwin, John J. (2023). "ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery". Journal of Chemical Information and Modeling. 63 (4): 1166–1176. doi:10.1021/acs.jcim.2c01253. PMC 9976280. PMID 36790087.
Warr, Wendy A.; Nicklaus, Marc C.; Nicolaou, Christos A.; Rarey, Matthias (2022). "Exploration of Ultralarge Compound Collections for Drug Discovery". Journal of Chemical Information and Modeling. 62 (9): 2021–2034. doi:10.1021/acs.jcim.2c00224. PMID 35421301.
Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2000). "Small Molecule Subgraph Detector (SMSD) toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.
Rahman, S. Asad; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2009). "Small Molecule Subgraph Detector (SMSD) Toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.
Butina, Darko (1999). "Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets". Chem. Inf. Comput. Sci. 39 (4): 747–750. doi:10.1021/ci9803381.
Pavlov, D.; Rybalkin, M.; Karulin, B. (2010). "Bingo from SciTouch LLC: Chemistry cartridge for Oracle database". Journal of Cheminformatics. 2 (Suppl 1): F1. doi:10.1186/1758-2946-2-S1-F1. PMC 2867114.

dotmatics.com

"Small Molecule Drug Discovery Software". Small Molecule Drug Discovery Software.
"Register". Archived from the original on 2021-12-10. Retrieved 2021-03-13.

ebi.ac.uk

"ChEMBL Database".
Rahman, S. Asad; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2009). "Small Molecule Subgraph Detector (SMSD) Toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.

harvard.edu

ui.adsabs.harvard.edu

Sadybekov, Anastasiia V.; Katritch, Vsevolod (2023). "Computational approaches streamlining drug discovery". Nature. 616 (7958): 673–685. Bibcode:2023Natur.616..673S. doi:10.1038/s41586-023-05905-z. PMID 37100941.
Ballester, P. J.; Richards, W. G. (2007). "Ultrafast shape recognition for similarity search in molecular databases". Proceedings of the Royal Society A. 463 (2081): 1307–1321. Bibcode:2007RSPSA.463.1307B. doi:10.1098/rspa.2007.1823. S2CID 12540483.
Jarabak, Charlotte; Mutton, Troy; Ridley, Damon D. (2020). "Property Information in Substance Records in Major Web-Based Chemical Information and Data Retrieval Tools: Understanding Content, Search Opportunities, and Application to Teaching". Journal of Chemical Education. 97 (5): 1345–1359. Bibcode:2020JChEd..97.1345J. doi:10.1021/acs.jchemed.9b00966.

macinchem.org

"Review of SDF Pro from Adroit DI. June 2023 – Macs in Chemistry". 2023-11-05. Retrieved 2024-03-11.

nih.gov

pubmed.ncbi.nlm.nih.gov

Harris, JB (2019). "Post-processing of Large Bioactivity Data". Bioinformatics and Drug Discovery. Methods Mol Biol. Vol. 1939. pp. 37–47. doi:10.1007/978-1-4939-9089-4_3. ISBN 978-1-4939-9088-7. PMID 30848455. S2CID 73493315.
Wang, Y; Bryant, SH; Cheng, T; Wang, J; Gindulyte, A; Shoemaker, BA; Thiessen, PA; He, S; Zhang, J (2017). "PubChem BioAssay: 2017 update". Nucleic Acids Res. 45 (D1): D955 – D963. doi:10.1093/nar/gkw1118. PMC 5210581. PMID 27899599.
Hoffmann, Torsten; Gastreich, Marcus (2019). "The next level in chemical space navigation: going far beyond enumerable compound libraries". Drug Discovery Today. 24 (5): 1148–1156. doi:10.1016/j.drudis.2019.02.013. PMID 30851414.
Sadybekov, Anastasiia V.; Katritch, Vsevolod (2023). "Computational approaches streamlining drug discovery". Nature. 616 (7958): 673–685. Bibcode:2023Natur.616..673S. doi:10.1038/s41586-023-05905-z. PMID 37100941.
Lin, Jr., Hung; Clark, Timothy (2005). "An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties". Journal of Chemical Information and Modeling. 45 (4): 1010–1016. doi:10.1021/ci050059v. PMID 16045295.
Meek, P. J.; Liu, Z.; Tian, L.; Wang, C. J; Welsh, W. J; Zauhar, R. J (2006). "Shape Signatures: speeding up computer aided drug discovery". DDT 2006. 19–20 (19–20): 895–904. doi:10.1016/j.drudis.2006.08.014. PMID 16997139.
Kim, Sunghwan (2021). "Exploring Chemical Information in PubChem". Current Protocols. 1 (8): e217. doi:10.1002/cpz1.217. PMC 8363119. PMID 34370395.
Ertl, Peter; Patiny, Luc; Sander, Thomas; et al. (2015). "Wikipedia Chemical Structure Explorer: Substructure and similarity searching of molecules from Wikipedia". Journal of Cheminformatics. 7: 10. doi:10.1186/s13321-015-0061-y. PMC 4374119. PMID 25815062.
Tingle, Benjamin I.; Tang, Khanh G.; Castanon, Mar; Gutierrez, John J.; Khurelbaatar, Munkhzul; Dandarchuluun, Chinzorig; Moroz, Yurii S.; Irwin, John J. (2023). "ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery". Journal of Chemical Information and Modeling. 63 (4): 1166–1176. doi:10.1021/acs.jcim.2c01253. PMC 9976280. PMID 36790087.
Warr, Wendy A.; Nicklaus, Marc C.; Nicolaou, Christos A.; Rarey, Matthias (2022). "Exploration of Ultralarge Compound Collections for Drug Discovery". Journal of Chemical Information and Modeling. 62 (9): 2021–2034. doi:10.1021/acs.jcim.2c00224. PMID 35421301.
Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2000). "Small Molecule Subgraph Detector (SMSD) toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.
Rahman, S. Asad; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2009). "Small Molecule Subgraph Detector (SMSD) Toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.

ncbi.nlm.nih.gov

Wang, Y; Bryant, SH; Cheng, T; Wang, J; Gindulyte, A; Shoemaker, BA; Thiessen, PA; He, S; Zhang, J (2017). "PubChem BioAssay: 2017 update". Nucleic Acids Res. 45 (D1): D955 – D963. doi:10.1093/nar/gkw1118. PMC 5210581. PMID 27899599.
Kim, Sunghwan (2021). "Exploring Chemical Information in PubChem". Current Protocols. 1 (8): e217. doi:10.1002/cpz1.217. PMC 8363119. PMID 34370395.
Ertl, Peter; Patiny, Luc; Sander, Thomas; et al. (2015). "Wikipedia Chemical Structure Explorer: Substructure and similarity searching of molecules from Wikipedia". Journal of Cheminformatics. 7: 10. doi:10.1186/s13321-015-0061-y. PMC 4374119. PMID 25815062.
Tingle, Benjamin I.; Tang, Khanh G.; Castanon, Mar; Gutierrez, John J.; Khurelbaatar, Munkhzul; Dandarchuluun, Chinzorig; Moroz, Yurii S.; Irwin, John J. (2023). "ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery". Journal of Chemical Information and Modeling. 63 (4): 1166–1176. doi:10.1021/acs.jcim.2c01253. PMC 9976280. PMID 36790087.
Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2000). "Small Molecule Subgraph Detector (SMSD) toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.
Rahman, S. Asad; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. (2009). "Small Molecule Subgraph Detector (SMSD) Toolkit". Journal of Cheminformatics. 1 (1): 12. doi:10.1186/1758-2946-1-12. PMC 2820491. PMID 20298518.
Pavlov, D.; Rybalkin, M.; Karulin, B. (2010). "Bingo from SciTouch LLC: Chemistry cartridge for Oracle database". Journal of Cheminformatics. 2 (Suppl 1): F1. doi:10.1186/1758-2946-2-S1-F1. PMC 2867114.

pubchem.ncbi.nlm.nih.gov

"PubChem". pubchem.ncbi.nlm.nih.gov.
"PubChem Structure Search". pubchem.ncbi.nlm.nih.gov. Retrieved 2024-08-01.

perkinelmerinformatics.com

"Signals Notebook - PerkinElmer Informatics". perkinelmerinformatics.com.

scilligence.com

"Scilligence RegMol | Scilligence". 6 June 2016. Archived from the original on September 29, 2018.

scrubchem.org

"Home Page - ScrubChem". scrubchem.org. Archived from the original on 26 May 2017.

semanticscholar.org

api.semanticscholar.org

Harris, JB (2019). "Post-processing of Large Bioactivity Data". Bioinformatics and Drug Discovery. Methods Mol Biol. Vol. 1939. pp. 37–47. doi:10.1007/978-1-4939-9089-4_3. ISBN 978-1-4939-9088-7. PMID 30848455. S2CID 73493315.
Grant, J. A; Gallardo, M. A.; Pickup, B. T. (1996). "A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape". Journal of Computational Chemistry. 17 (14): 1653–1666. doi:10.1002/(sici)1096-987x(19961115)17:14<1653::aid-jcc7>3.0.co;2-k. S2CID 96794688.
Ballester, P. J.; Richards, W. G. (2007). "Ultrafast shape recognition for similarity search in molecular databases". Proceedings of the Royal Society A. 463 (2081): 1307–1321. Bibcode:2007RSPSA.463.1307B. doi:10.1098/rspa.2007.1823. S2CID 12540483.

web.archive.org

"Home Page - ScrubChem". scrubchem.org. Archived from the original on 26 May 2017.
"Register". Archived from the original on 2021-12-10. Retrieved 2021-03-13.
"Scilligence RegMol | Scilligence". 6 June 2016. Archived from the original on September 29, 2018.

wipo.int

"Substructure Search Now Available in PATENTSCOPE". www.wipo.int. 2019-02-11. Retrieved 2024-08-04.