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 may be helpful for various studies on molecular recognition occurred in biological systems.

The PDBbind database was orginally 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 at this web site, i.e. PDBbind-CN, by Prof. Renxiao Wang's group (http://www.sioc-ccbg.ac.cn) at the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences in China under a mutual agreement with the University of Michigan. All registered users of the original PDBbind database have been granted access to the PDBbind-CN web site as well.

Current release. The PDBbind database is updated on an annual base to keep up with the growth of the Protein Data Bank. The current release, i.e. version 2014, is based on the contents of Protein Data Bank officially released on Jan 1st, 2014. This version provides binding affinity data and structural information for a total of 12,995 biomolecular complexes, including protein-ligand (10656), nucleic acid-ligand (87), protein-nucleic acid (660), and protein-protein complexes (1592), which is the largest collection of this kind so far. Binding data included in version 2014 have increased by 20.6% as compared to version 2013. All of these data are collected from >28,000 original references by ourselves. They all have been double-checked to ensure that they match the complex structures in the Protein Data Bank. Moreover, a "refined set" and a "core set" are compiled as high-quality data sets of protein-ligand complexes for docking/scoring studies. 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 browsing, i.e. users do not need registration to access the "BROWSE" page. However, users are required to register under a license agreement in order to utilize the full functions provided on the other pages at this web site, e.g. searching engines, or to download the contents of PDBbind in bulk. The registration is free of charge to all academic and industrial users. Please go to the "[REGISTER]" page and follow the instructions to register.

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1. FAQs of the PDBbind-CN database
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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.

[2] 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.

[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.

[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.

[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.

[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.

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