Welcome to the PDBbind-CN Database!

Introduction. The aim of the PDBbind database is to provide a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank (PDB). It provides an essential linkage between the energetic and structural information of those complexes, which is helpful for various computational and statistical studies on molecular recognition, drug discovery, and many more (see the list of published applications of PDBbind).

The PDBbind database was originally developed by Prof. Shaomeng Wang's group at the University of Michigan in USA, which was first released to the public in May, 2004. This database is now maintained and further developed by Prof. Renxiao Wang's group at College of Pharmacy, Fudan University in China. The PDBbind database is updated on an annual base to keep up with the growth of the Protein Data Bank.

Invitation to the new PDBbind+ web site 02/03/2024

Current release. The current release, i.e. version 2020, is based on the contents of PDB officially released at the first week in 2020. This release provides binding affinity data for a total of 23,496 biomolecular complexes in PDB, including protein-ligand (19,443), protein-protein (2,852), protein-nucleic acid (1,052), and nucleic acid-ligand complexes (149). Compared to the last release (v.2019), binding data included in this release have increased by ~10%. All binding data are curated by ourselves from ~40,500 original references. Click here for a brief introduction to the PDBbind database (PDF).

A special remark on the PDBbind core set. Compilation of the PDBbind core set aims at providing a relatively small set of high-quality protein-ligand complexes for validating docking/scoring methods. The data set is selected based on the contents of PDBbind. In particular, this data set has served as the primary test set in the popular Comparative Assessment of Scoring Functions (CASF) benchmark developed by our group. The PDBbind core set is not included in the PDBbind data package because it is not updated annually as PDBbind itself. Users can obtain the PDBbind core set by downloading the CASF data package at http://www.pdbbind.org.cn/casf.php. The latest available version of the PDBbind core set is included in CASF-2016, which consists of 285 protein-ligand complexes.

Accessibility. The basic information of each complex in PDBbind is completely open for access (see the [BROWSE] page). Users are required to register under a license agreement in order to utilize the searching functions provided on this web site or to download PDBbind data sets in bulk. Registration is currently free of charge to all academic and industrial users. Please go to the [REGISTER] page and follow the instructions to complete registration.

Acknowledgments. This project is financially supported by the Ministry of Science and Technology of China (National Key Research Program, Grant No. 2016YFA0502302) and the National Natural Science Foundation of China (Grant No. 81725022, 81430083, 21661162003, 21673276, 21472227, 21472226). We are very grateful to Prof. Zenghui (John) Zhang's group at the East China Normal University for their aid to version 2015, 2016, and 2017.

News & Notice

Invitation to the new PDBbind+ web site (02/03/2024)

Dear All, We are excited to announce that the beta version of our new PDBbind+ web site is now ready for test. Starting from version 2021, all future new versions of the PDBbind database will be released solely on PDBbind+. We cordially invite you to experience the upgraded features of the PDBbind+ web site. Current registered PDBbind users will be receiving an e-mail soon, from which his/her account on PDBbind+ can be activated directly after transferring his/her user profile on PDBbind-CN to the new web site. Others are encouraged to visit PDBbind+ at www.pdbbind-plus.org.cn. Registration on the PDBbind+ web site as a demo user is FREE. Demo users may access the contents of the PDBbind database up to version 2020 on the new web site. We plan to release version 2021, as well as additional functional modules, on PDBbind+ once the beta test is completed. Official release of version 2021 is anticipated in this month, so please stay tuned. For the sake of current PDBbind users, the PDBbind-CN web site will still be up running as is, but no future update of PDBbind-CN is planned. If you need any assistance or have any questions regarding PDBbind+, please feel free to reach us at support@pdbbind-plus.org.cn. Thank you for your continued support to the PDBbind database! Best regards, The PDBbind Team School of Pharmacy, Fudan University

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Team Leader: Prof. Renxiao Wang
Email: wangrx@fudan.edu.cn
Tel: +86-21-54925128
Support: yingsaisi@foxmail.com

The PDBbind-CN Team Members

[1] Minyi Su, Qifan Yang, Yu Du, Guoqin Feng, Zhihai Liu, Yan Li,* Renxiao Wang,*, "Comparative Assessment of Scoring Functions: The CASF-2016 Update", J. Chem. Inf. Model, 2019, Vol. 59: pp 895-913.(CASF-2016)

[2] Yan Li, Minyi Su, Zhihai Liu, Jie Li, Jie Liu, Li Han, Renxiao Wang *, "Assessing Protein-Ligand Interaction Scoring Functions with the CASF-2013 Benchmark", Nature Protocols, 2018, Vol. 3(4): pp 666-680.(CASF-2013)

[3] Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao *, "Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions", Accounts of Chemical Research, 2017, 50 (2): pp. 302-309.(PDBbind version 2016)

[4] Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao, Wei Nie, Yuchen Liu and Renxiao Wang, "PDB-wide collection of binding data: current status of the PDBbind database", Bioinformatics, 2015, 31 (3): 405-412. (PDBbind version 2014)

[5] Li Y.; Liu Z.H.; Li J.; Han L.; Liu J.; Zhao Z.X.; Wang R.X. "Comparative Assessment of Scoring Functions on an Updated Benchmark: I. Compilation of the Test Set", J. Chem. Inf. Model., 2014, 54 (6), pp. 1700-1716. (PDBbind version 2013)

[6] Li, Y.; Han, L.; Liu, Z. H.; Wang, R. X.*. "Comparative Assessment of Scoring Functions on an Updated Benchmark: II. Evaluation Methods and General Results", J. Chem. Inf. Model., 2014, 54 (6), pp. 1717-1736. (CASF-2013)

[7] Cheng T.J.; Li X.; Li Y.; Liu Z.H.; Wang R.X. "Comparative assessment of scoring functions on a diverse test set", J. Chem. Inf. Model., 2009; 49(4); 1079-1093. (PDBbind version 2007)

[8] Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. "The PDBbind Database: Methodologies and updates", J. Med. Chem., 2005; 48(12); 4111-4119. (PDBbind prototype)

[9] Wang, R.; Fang, X.; Lu, Y.; Wang, S. "The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures", J. Med. Chem., 2004; 47(12); 2977-2980. (PDBbind prototype)

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