Welcome to the PDBbind-CN Database!

Introduction. The aim of the PDBbind database is to provide a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). It thus provides an essential linkage between energetic and structural information of these complexes, which is helpful for various computational and statistical studies on molecular recognition occurred in biological systems.

The PDBbind database was originally developed by Prof. Shaomeng Wang's group at the University of Michigan (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 the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences. The PDBbind database is now updated on an annual base to keep up with the growth of the Protein Data Bank.

Current release. The current release, i.e. version 2019, is based on the contents of PDB officially released by Jan 1st, 2019. This release provides binding data of a total of 21,382 biomolecular complexes, including protein-ligand (17,679), nucleic acid-ligand (136), protein-nucleic acid (973), and protein-protein complexes (2,594), which is currently the largest collection of this kind. Compared to the last release (v.2018), binding data included in this release have increased by 9.2%. All binding data are curated by ourselves from over 37,000 original references. Moreover, a "refined set" of high-quality protein-ligand complexes is compiled as the data basis for developing and validating docking/scoring methods. Click here for a brief introduction to the PDBbind database (PDF brochure).
A Special Statement about the PDBbind core set and the CASF benchmark Mar 3rd, 2018

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 the contents of PDBbind in bulk. Registration is 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), the National Natural Science Foundation of China (Grant No. 81725022, 81430083, 21661162003, 21673276, 21472227, and 21472226), and Chinese Academy of Sciences (Strategic Priority Research Program, Grant No. XDB20000000). 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

1. The PDBbind version 2019 is just released (01/12/2020)

2. The PDBbind version 2018 is just released (12/10/2018)

3. The PDBbind version 2017 is just released (12/19/2017)

4. The PDBbind version 2016 is just released (12/08/2016)

5. The PDBbind database version 2015 is just released (12/16/2015)

6. The PDBbind version 2015 is under way ... finally (11/23/2015)

7. The PDBbind database version 2014 is just released (09/22/2014)

8. The PDBbind database version 2013 is released now (11/22/2013)

9. PDBbind version 2013 is under way ... (07/16/2013)

10. The PDBbind database version 2012 is released now (10/30/2012)

11. Small-molecule ligands have been updated (08/31/2012)

12. PDBbind v2011 is released now (09/22/2011)

13. PDBbind v2011 is under way (08/03/2011)

14. New domain name of PDBbind (02/28/2011)

15. PDBbind v2010 is now released (10/25/2010)

16. Small-molecule ligands have been updated (01/29/2010)

17. Please deposit binding affinity data! (01/04/2010)

18. PDBbind v2009 is now released (12/24/2009)

19. PDBbind v2009 is under way (10/01/2009)

20. Small-molecule ligands in PDB have been updated (01/15/2009)

21. All small-molecule ligands in PDB are available for searching now (10/30/2008)

22. Mutual links between PDBbind-CN and PDBsum are added (10/08/2008)

23. PDBbind v.2008 is released (09/10/2008)

24. The PDBbind-CN server is launched! (11/2007)

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4. Deposit binding affinity data into PDBbind-CN

Group Leader: Prof. Renxiao Wang
Email: wangrx@fudan.edu.cn
Tel: +86-21-54925128
Support: liuhai@mail.sioc.ac.cn

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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