BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Liu, Tiqing; Hwang, Linda; Burley, Stephen K.; Nitsche, Carmen I.; Southan, Christopher; Walters, W. Patrick; Gilson, Michael K.

doi:10.1093/nar/gkae1075

Title: BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Journal Article · 21 November 2024 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkae1075 · OSTI ID:2478579

Liu, Tiqing; Hwang, Linda; Burley, Stephen K.; Nitsche, Carmen I.; Southan, Christopher; Walters, W. Patrick;

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0019749

OSTI ID:: 2478579

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 53; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (51)

Generative Recurrent Networks for De Novo Drug Design Gupta, Anvita; Müller, Alex T.; Huisman, Berend J. H. Molecular Informatics, Vol. 37, Issue 1-2 https://doi.org/10.1002/minf.201700111	journal	November 2017
Risperidone compared with new and reference antipsychotic drugs: in vitro and in vivo receptor binding Schotte, A.; Janssen, P. F. M.; Gommeren, W. Psychopharmacology, Vol. 124, Issue 1-2 https://doi.org/10.1007/BF02245606	journal	March 1996
Generative chemistry: drug discovery with deep learning generative models Bian, Yuemin; Xie, Xiang-Qun Journal of Molecular Modeling, Vol. 27, Issue 3 https://doi.org/10.1007/s00894-021-04674-8	journal	February 2021
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions Gathiaka, Symon; Liu, Shuai; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 30, Issue 9 https://doi.org/10.1007/s10822-016-9946-8	journal	September 2016
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies Gaieb, Zied; Liu, Shuai; Gathiaka, Symon Journal of Computer-Aided Molecular Design, Vol. 32, Issue 1 https://doi.org/10.1007/s10822-017-0088-4	journal	December 2017
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings Gaieb, Zied; Parks, Conor D.; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 33, Issue 1 https://doi.org/10.1007/s10822-018-0180-4	journal	January 2019
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies Parks, Conor D.; Gaieb, Zied; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 34, Issue 2 https://doi.org/10.1007/s10822-020-00289-y	journal	January 2020
Molecular biology of 5-HT receptors Boess, F. G.; Martin, I. L. Neuropharmacology, Vol. 33, Issue 3-4 https://doi.org/10.1016/0028-3908(94)90059-0	journal	March 1994
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80200-3	journal	May 1977
The Synthesizability of Molecules Proposed by Generative Models Gao, Wenhao; Coley, Connor W. Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c00174	journal	April 2020
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma Carlson, Heather A.; Smith, Richard D.; Damm-Ganamet, Kelly L. Journal of Chemical Information and Modeling, Vol. 56, Issue 6 https://doi.org/10.1021/acs.jcim.5b00523	journal	May 2016
Abolishing Dopamine D_2long/D₃ Receptor Affinity of Subtype-Selective Carbamoylguanidine-Type Histamine H₂ Receptor Agonists Tropmann, Katharina; Bresinsky, Merlin; Forster, Lisa Journal of Medicinal Chemistry, Vol. 64, Issue 12 https://doi.org/10.1021/acs.jmedchem.1c00692	journal	June 2021
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules Weininger, David Journal of Chemical Information and Modeling, Vol. 28, Issue 1 https://doi.org/10.1021/ci00057a005	journal	February 1988
CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes Dunbar, James B.; Smith, Richard D.; Yang, Chao-Yie Journal of Chemical Information and Modeling, Vol. 51, Issue 9 https://doi.org/10.1021/ci200082t	journal	July 2011
Generative Models as an Emerging Paradigm in the Chemical Sciences Anstine, Dylan M.; Isayev, Olexandr Journal of the American Chemical Society, Vol. 145, Issue 16 https://doi.org/10.1021/jacs.2c13467	journal	April 2023
The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures Wang, Renxiao; Fang, Xueliang; Lu, Yipin Journal of Medicinal Chemistry, Vol. 47, Issue 12 https://doi.org/10.1021/jm030580l	journal	June 2004
CoMFA and CoMSIA Analyses of Pneumocystis carinii Dihydrofolate Reductase, Toxoplasma gondii Dihydrofolate Reductase, and Rat Liver Dihydrofolate Reductase Gangjee, Aleem; Lin, Xin Journal of Medicinal Chemistry, Vol. 48, Issue 5 https://doi.org/10.1021/jm040153n	journal	February 2005
The PDBbind Database: Methodologies and Updates Wang, Renxiao; Fang, Xueliang; Lu, Yipin Journal of Medicinal Chemistry, Vol. 48, Issue 12 https://doi.org/10.1021/jm048957q	journal	June 2005
The Properties of Known Drugs. 1. Molecular Frameworks Bemis, Guy W.; Murcko, Mark A. Journal of Medicinal Chemistry, Vol. 39, Issue 15 https://doi.org/10.1021/jm9602928	journal	January 1996
2020 FDA drug approvals Mullard, Asher Nature Reviews Drug Discovery, Vol. 20, Issue 2 https://doi.org/10.1038/d41573-021-00002-0	journal	January 2021
A small molecule–kinase interaction map for clinical kinase inhibitors Fabian, Miles A.; Biggs, William H.; Treiber, Daniel K. Nature Biotechnology, Vol. 23, Issue 3 https://doi.org/10.1038/nbt1068	journal	February 2005
Quantifying the chemical beauty of drugs Bickerton, G. Richard; Paolini, Gaia V.; Besnard, Jérémy Nature Chemistry, Vol. 4, Issue 2 https://doi.org/10.1038/nchem.1243	journal	January 2012
PatCID: an open-access dataset of chemical structures in patent documents Morin, Lucas; Weber, Valéry; Meijer, Gerhard Ingmar Nature Communications, Vol. 15, Issue 1 https://doi.org/10.1038/s41467-024-50779-y	journal	August 2024
Assessing the impact of generative AI on medicinal chemistry Walters, W. Patrick; Murcko, Mark Nature Biotechnology, Vol. 38, Issue 2 https://doi.org/10.1038/s41587-020-0418-2	journal	January 2020
How will generative AI disrupt data science in drug discovery? Vert, Jean-Philippe Nature Biotechnology, Vol. 41, Issue 6 https://doi.org/10.1038/s41587-023-01789-6	journal	May 2023
Molecular design in drug discovery: a comprehensive review of deep generative models Cheng, Yu; Gong, Yongshun; Liu, Yuansheng Briefings in Bioinformatics, Vol. 22, Issue 6 https://doi.org/10.1093/bib/bbab344	journal	August 2021
PDB-wide collection of binding data: current status of the PDBbind database Liu, Zhihai; Li, Yan; Han, Li Bioinformatics, Vol. 31, Issue 3 https://doi.org/10.1093/bioinformatics/btu626	journal	October 2014
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
PubChem in 2021: new data content and improved web interfaces Kim, Sunghwan; Chen, Jie; Cheng, Tiejun Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa971	journal	November 2020
UniProt: the Universal Protein Knowledgebase in 2023 Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1052	journal	November 2022
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1077	journal	November 2022
PubChem 2023 update Kim, Sunghwan; Chen, Jie; Cheng, Tiejun Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac956	journal	October 2022
The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods Zdrazil, Barbara; Felix, Eloy; Hunter, Fiona Nucleic Acids Research, Vol. 52, Issue D1 https://doi.org/10.1093/nar/gkad1004	journal	November 2023
UniProt: the Universal Protein knowledgebase Apweiler, R. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh131	journal	January 2004
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Liu, T.; Lin, Y.; Wen, X. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl999	journal	January 2007
PubChem's BioAssay Database Wang, Y.; Xiao, J.; Suzek, T. O. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1132	journal	December 2011
ChEMBL: a large-scale bioactivity database for drug discovery Gaulton, A.; Bellis, L. J.; Bento, A. P. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr777	journal	September 2011
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1214	journal	November 2014
UniProt: a hub for protein information Consortium, UniPot Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212 https://doi.org/10.1093/nar/gku989	journal	October 2014
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology Gilson, Michael K.; Liu, Tiqing; Baitaluk, Michael Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1072	journal	October 2015
SureChEMBL: a large-scale, chemically annotated patent document database Papadatos, George; Davies, Mark; Dedman, Nathan Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1253	journal	November 2015
The ChEMBL database in 2017 Gaulton, Anna; Hersey, Anne; Nowotka, Michał Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1074	journal	November 2016
PubChem 2019 update: improved access to chemical data Kim, Sunghwan; Chen, Jie; Cheng, Tiejun Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1033	journal	October 2018
A Multifactorial Approach to Hepatobiliary Transporter Assessment Enables Improved Therapeutic Compound Development Morgan, Ryan E.; van Staden, Carlo J.; Chen, Yuan Toxicological Sciences, Vol. 136, Issue 1 https://doi.org/10.1093/toxsci/kft176	journal	August 2013
Mitigating the Inhibition of Human Bile Salt Export Pump by Drugs: Opportunities Provided by Physicochemical Property Modulation, In Silico Modeling, and Structural Modification Warner, Daniel J.; Chen, Hongming; Cantin, Louis-David Drug Metabolism and Disposition, Vol. 40, Issue 12 https://doi.org/10.1124/dmd.112.047068	journal	September 2012
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions Ertl, Peter; Schuffenhauer, Ansgar Journal of Cheminformatics, Vol. 1, Issue 1 https://doi.org/10.1186/1758-2946-1-8	journal	June 2009
InChI, the IUPAC International Chemical Identifier Heller, Stephen R.; McNaught, Alan; Pletnev, Igor Journal of Cheminformatics, Vol. 7, Issue 1 https://doi.org/10.1186/s13321-015-0068-4	journal	May 2015
Reinvent 4: Modern AI–driven generative molecule design Loeffler, Hannes H.; He, Jiazhen; Tibo, Alessandro Journal of Cheminformatics, Vol. 16, Issue 1 https://doi.org/10.1186/s13321-024-00812-5	journal	February 2024
BindingDB: A Web-Accessible Molecular Recognition Database Chen, Xi; Liu, Ming; Gilson, Michael Combinatorial Chemistry & High Throughput Screening, Vol. 4, Issue 8 https://doi.org/10.2174/1386207013330670	journal	December 2001
Chronopolis Digital Preservation Network Minor, David; Sutton, Don; Kozbial, Ardys International Journal of Digital Curation, Vol. 5, Issue 1 https://doi.org/10.2218/ijdc.v5i1.147	journal	June 2010
CoreTrustSeal: From academic collaboration to sustainable services L'Hours, Hervé; Kleemola, Mari; De Leeuw, Lisa IASSIST Quarterly, Vol. 43, Issue 1 https://doi.org/10.29173/iq936	journal	May 2019

Similar Records

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Journal Article · 2021 · Bioinformatics · OSTI ID:1844289

Bittrich, Sebastian; Rose, Yana; Segura, Joan; +5 more

Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

Technical Report · 2014 · OSTI ID:1163480

Sjolander, Kimmen

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Journal Article · 2024 · Database · OSTI ID:2426666

Xu, Chunhui; Shaw, Trey; Choppararu, Sai Akhil; +16 more

Title: BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Citation Formats

References (51)

Similar Records

Related Subjects