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 2017, is based on the contents of PDB officially released by Jan 1st, 2017. This release provides binding data of a total of 17,900 biomolecular complexes, including protein-ligand (14,761), nucleic acid-ligand (121), protein-nucleic acid (837), and protein-protein complexes (2,181), which is currently the largest collection of this kind. Compared to the last release (v.2016), binding data included in this release have increased by 10.64%. All binding data are curated by ourselves from over 32,000 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 2015,2016,2017.

News & Notice

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

Dear Users,

We are about to finish PDBbind version 2015. This update is significantly delayed as compared to previous ones due to a number of reasons. But the good news is that we are approaching to the last stage, and we will release this new update before the end of this year.

To give you some basic information, this update is based on the 105,183 entries release by PDB in Jan 2015. A total number of 48,821 valid complexes identified, and binding data are available for 14,620 of them. We also plan to provide the processed structural files of all valid protein-ligand complexes, no matter their binding data are available or not, in near future.

Best regards,

The PDBbind-CN team

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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] 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)

[2] 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)

[3] 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)

[4] 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)

[5] 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)

[6] 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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