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 (http://sw16.im.med.umich.edu) 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 (http://www.sioc-ccbg.ac.cn) at the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences under a mutual agreement with the University of Michigan. 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 2016, is based on the contents of PDB officially released by Jan 1st, 2016. This release provides binding data of a total of 16,179 biomolecular complexes, including protein-ligand (13,308), nucleic acid-ligand (118), protein-nucleic acid (777), and protein-protein complexes (1,976), which is currently the largest collection of this kind. Compared to the last release (v.2015), binding data included in this release have increased by 10.66%. All binding data are curated by ourselves from over 29,000 original references. Moreover, a "refined set" and a "core set" are compiled as high-quality data sets of protein-ligand complexes for developing and validating docking/scoring methods. Click here for a brief introduction to the PDBbind database (PDF brochure).

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 National Natural Science Foundation of China (grants #81430083, #81172984, #21072213, #21102168, #21402230). We are very grateful to Prof. Zenghui (John) Zhang's group at East China Normal University for their aid to the collection of raw data needed by version 2015,2016.

News & Notice

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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5. Deposit binding affinity data into PDBbind-CN

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

The PDBbind-CN Team Members

[1] 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)

[2] 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)

[3] 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)

[4] 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 early versions)

[5] 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 early versions)

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