BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. BindingDB (http://www.bindingdb.org) is a publicly accessible database currently containing approximately 20,000 experimentally determined binding affinities of protein-ligand complexes, for 110 protein targets including isoforms and mutational variants, and approximately 11,000 small molecule ligands. The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data Bank. The BindingDB website supports a range of query types, including searches by chemical structure, substructure and similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. Data sets generated by BindingDB queries can be downloaded in the form of annotated SDfiles for further analysis, or used as the basis for virtual screening of a compound database uploaded by the user. The data in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs.
Keywords for this software
References in zbMATH (referenced in 7 articles , 1 standard article )
Showing results 1 to 7 of 7.
- Haiping Lu, Xianyuan Liu, Robert Turner, Peizhen Bai, Raivo E Koot, Shuo Zhou, Mustafa Chasmai, Lawrence Schobs: PyKale: Knowledge-Aware Machine Learning from Multiple Sources in Python (2021) arXiv
- Tutone, Marco; Virzì, Alessia; Almerico, Anna Maria: Reverse screening on indicaxanthin from \textitOpuntiaficus-indica as natural chemoactive and chemopreventive agent (2018)
- Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
- Yan, Cheng; Wang, Jianxin; Lan, Wei; Wu, Fang-Xiang; Pan, Yi: SDTRLS: predicting drug-target interactions for complex diseases based on chemical substructures (2017)
- Wang, Xiaohong; Huan, Jun; Smalter, Aaron M.; Lushington, Gerald H.: Application of kernel functions for accurate similarity search in large chemical databases (2010) ioport
- Gardiner, Eleanor J.; Gillet, Valerie J.; Haranczyk, Maciej; Hert, Jérôme; Holliday, John D.; Malim, Nurul; Patel, Yogendra; Willett, Peter: Turbo similarity searching: effect of fingerprint and dataset on virtual-screening performance (2009)
- Liu, Tiqing; Lin, Yuhmei; Wen, Xin; Jorissen, Robert N.; Gilson, Michael K.: Bindingdb: a web-accessible database of experimentally determined protein-ligand binding affinities. (2007) ioport