Welcome to PDBbind-CN Database
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 2018, is based on the contents of PDB officially released by Jan 1st, 2018. This release provides binding data of a total of 19,588 biomolecular complexes, including protein-ligand (16,151), nucleic acid-ligand (125), protein-nucleic acid (896), and protein-protein complexes (2,416), which is currently the largest collection of this kind. Compared to the last release (v.2017), binding data included in this release have increased by 9.43%. All binding data are curated by ourselves from over 34,700 original references. Moreover, a "refined set" and a "core set(now CASF)" 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).
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 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



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

Dear researchers,

The PDBbind database aims at providing a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank. Since its first public release in 2004, this database has been used by thousands of researchers all across the world. This database is now upadted annually by our group to keep up with the growth of the Protein Data Bank.

Here, we are happy to announce another release of the PDBbind database, i.e. version 2009. This version provides binding affinity data and structural information for a total of 5,678 biomolecular complexes, including protein-ligand (4277), nucleic acid-ligand (44), protein-nucleic acid (304), and protein-protein complexes (1053), which is the largest collection of this kind so far. Binding data included in version 2009 have increased by 30% as compared to version 2008. All of these data are collected from original references by ourselves. They all have been double-checked to ensure that they match the complex structures in the Protein Data Bank.

The PDBbind version 2009 is now available on the PDBbind-CN server at http://www.pdbbind.org.cn/. The basic information of each complex in PDBbind is totally open for browsing. Users are required to register with a license agreement if they want to use the full functions provided on our web site. Registration is free of charge to all academic and industrial users. We also love to hear your comments so that we can do a better job for next release!

Best regards,

Prof. Renxiao Wang
Shanghai Institute of Organic Chemistry
Chinese Academy of Sciences
Shanghai, P. R. China

User E-mail
Password
  
Register    Forget Password?

1. FAQs of the PDBbind-CN database
2. Feedback to the PDBbind-CN team
3. Post open access message on our forum page
4. Register a new account in PDBbind-CN
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] 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)

[2] 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)

[3] 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)

[4] 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)

[5] 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)

[6] 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)

[7] 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)

This site has been visited times since Nov 2007.


Address: LingLing Road 345, Shanghai, 200032, China      ICP NO: Shanghai-05005485-2
Group Leader: wangrx@mail.sioc.ac.cn      Tel: +86-21-54925128      Webmaster: liuhai@mail.sioc.ac.cn
Copyright ©2007-2019    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences