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.
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What's New

Data updated (Sep. 17, 2014).

We have a data update. Please see the Statistics.

New version of interface (Nov. 2, 2012).

We improved the Web interface for better search, navigation and visualization. Please see the Tutorial.

Integration of structural and biochemical interaction information (Nov. 2, 2012).

We integrated protein-protein interaction information obtained by biochemical experiments into PDBnet. Please see the Feature Highlight.

Domain and non-domain interactions in PPI (Nov. 2, 2012).

We added interactions among domains and non-domains within protein-protein interaction (PPI) network. Please see the Feature Highlight.

Biological unit (Nov. 2, 2012).

We now use Biological Unit in PDB for constructing interactions and networks. Thus, the total number was reduced from the last update.

Data updated (Nov. 2, 2012).

We have a major update. Please see the Feature Highlight. For more information about this update, please see the Statistics.

Data updated (Feb. 23, 2011).

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

Data updated (Nov. 19, 2010).

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

Data updated (Apr. 28, 2010).

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

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

Integration of structural and biochemical interaction information

Protein-protein interaction (PPI) information from structural data is integrated with that obtained by biochemical experiments. For a protein cluster of interest, interacting clusters are shown as a diagram, along with detailed information of biochemical experimental data including reliability score, amino-acid sequences and structures (if available) for each pair of interacting clusters. The red nodes in the diagram represent protein clusters observed in both structural PPI and biochemical PPI. This feature will be useful for easily identifying what are missing interactions in the structurome and what is available structural information in the PPI network. See the Tutorial for more detail.

Domain and non-domain interactions in PPI

Structural data can provide detailed information about the interactions within PPI. We analyzed inter-chain interactions among domains and non-domains contained in all the complex structures, and visualized as a diagram along with the corresponding structure. This feature will be useful for examining which domains and non-domain regions of each chain are involved in the interactions within PPI. See the Tutorial for more detail.

Tutorial page here.

Statistics

Date (yy/mm/dd) PDB entries chains clusters cluster links(physical contacts) networks protein chains nucleic acid chains clusters linked with nucleic acids networks containing nucleic acids Biochemical PPI
Page
14/09/17 103,262 291,015 23,167 41,749 (16,414) 10,559 272,972 18,043 1,875 598 824,803
12/11/02 85,848 229,842 28,152 34,879 (17,588) 14,119 215,358 14,484 1,507 572 571,617
11/02/23 71,070 185,479 24,328 14,102 (4,797) 1,234 173,573 11,906 1,271 98
10/11/19 68,994 178,637 23,656 11,378 (4,462) 1,210 167,173 11,464 1,208 98
10/04/28 64,385 164,468 22,296 11,293 (4,452) 1,102 153,798 10,670 1,154 93
09/08/08 59,330 148,469 20,794 10,506 (4,302) 1,078 138,554 9,915 1,094 88
09/04/15 57,013 141,837 19,989 10,238 (4,146) 1,053 132,278 9,559 1,071 89
09/01/10 55,126 136,770 19,325 9,977 (4,010) 1,026 127,443 9,327 1,038 81
08/10/04 53,392 131,719 18,762 9,804 (3,901) 991 122,679 9,040 1,014 78
08/06/09 51,163 125,648 17,956 9,557 (3,745) 955 116,949 8,699 988 77
08/04/01 49,768 121,576 17,385 8,298 (3,594) 932 113,113 8,463 880 73
07/12/14 47,813 116,717 17,660 11,801 (4,534) 970 108,437 8,280 876 71
07/09/28 46,385 113,250 17,056 11,335 (4,364) 945 105,165 8,085 866 71
07/07/20 44,848 108,824 16,370 11,197 (4,281) 919 100,952 7,872 854 69
07/03/23 42,474 102,703 15,475 10,956 (4,079) 883 95,178 7,525 837 69
06/07/21 37,981 90,806 13,621 9,808 (----) 804 83,945 6,861 752 61