PDBnet Bird's eye view of network in structurome

Overview of PDBnet

Most of biological functions are achieved by cooperative action of huge number of molecules in the network such as signal transduction and metabolic networks. In order to understand the molecular mechanism of the cooperative action in the molecular network and to develop drugs, structural information of molecules and their interactions are essential. There are a large number of biomolecular structures registered in Protein Data Bank (PDB). The biomolecular structural space (structurome) is not only expanding but also becoming more complex, which makes it harder to extract useful information. Thus, we have developed a database/tool of biomolecular network, PDBnet, based on the structural information of PDB. PDBnet will provide a bird's-eye view of molecular organization in the structurome, and enable users to extract various kinds of information about structures, interactions and networks of biomolecules.

What's New

New version of interface (Aug. 10, 2009).

We updated the Web interface for better search, navigation and visualization. One of the new features is Integrated View. Please see the Feature Highlight.

Data updated (Aug. 8, 2009).

For more information about this update, please see the Statistics.

Data updated (Apr. 15, 2009).

For more information about this update, please see the Statistics.

Data updated (Jan. 10, 2009).

For more information about this update, please see the Statistics.

Data updated (Oct. 4, 2008).

For more information about this update, please see the Statistics.

Data updated (Jun. 9, 2008).

For more information about this update, please see the Statistics.

Data updated (Dec. 14, 2007).

For more information about this update, please see the Statistics.

Data updated (Sep. 28, 2007).

For more information about this update, please see the Statistics.

Data updated (July. 20, 2007).

For more information about this update, please see the Statistics.

The links with physical contacts (June 22, 2007).

The links among clusters in PDBnet are based on the co-occurrence in the same PDB structures. However, it does not mean that the chains within the same PDB structures are physically interacting. We analyzed the physical contacts among all the chains in the PDB structures. Those links with physical contacts (within 4 A distance) in the network are shown in red color. For the number of those links, please see the Statistics page.

Data updated (Mar 23, 2007).

For more information about this update, please see the Statistics. Please note that cluster and network IDs and their memberships may be different from the previous version. The cluster and network IDs for all the chains in the old and new versions can be viewed at the Statistics page.

Release of PDBnet (Nov. 30, 2006).

The first version of PDBnet is Released.

Feature Highlight

Integrated View

PDBnet provides an integrated view page displaying the network graph, complex structure, and sequence alignment of chains within the core cluster (the central cluster in the network) with mapped interacting residues. For more information, please see the Tutorial page here.

Statistics

Date PDB entries chains clusters cluster links
(physical contacts)		 networks protein chains nucleic acid chains clusters linked with nucleic acids networks containing nucleic acids details of chains
Page
100428 64,385 164,468 22,296 11,293 (4,452) 1,102 153,798 10,670 1154 93 details
090808 59,330 148,469 20,794 10,506 (4,302) 1,078 138,554 9,915 1094 88 details
090415 57,013 141,837 19,989 10,238 (4,146) 1,053 132,278 9,559 1071 89 details
090110 55,126 136,770 19,325 9,977 (4,010) 1,026 127,443 9,327 1038 81 details
081004 53,392 131,719 18,762 9,804 (3,901) 991 122,679 9,040 1014 78 details
080609 51,163 125,648 17,956 9,557 (3,745) 955 116,949 8,699 988 77 details
080401 49,768 121,576 17,385 8,298 (3,594) 932 113,113 8,463 880 73 details
071214 47,813 116,717 17,660 11,801 (4,534) 970 108,437 8,280 876 71 details
070928 46,385 113,250 17,056 11,335 (4,364) 945 105,165 8,085 866 71 details
070720 44,848 108,824 16,370 11,197 (4,281) 919 100,952 7,872 854 69 details
070323 42,474 102,703 15,475 10,956 (4,079) 883 95,178 7,525 837 69 details
060721 37,981 90,806 13,621 9,808 (----) 804 83,945 6,861 752 61 details