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. 2009 Jan;37(Database issue):D360-4.
doi: 10.1093/nar/gkn659. Epub 2008 Oct 4.

PiSite: a database of protein interaction sites using multiple binding states in the PDB

Miho Higurashi  1 , Takashi Ishida, Kengo Kinoshita
Affiliations

PiSite: a database of protein interaction sites using multiple binding states in the PDB

Miho Higurashi et al. Nucleic Acids Res. 2009 Jan.

Abstract

The vast accumulation of protein structural data has now facilitated the observation of many different complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein-protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein-protein interfaces. PiSite is available at http://pisite.hgc.jp.

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Figures

Figure 1.
Figure 1.
An explanation of residue mapping. The upper panel shows a schematic representation of residue mapping, and the lower panel shows an example of the mapping by using 3D models. In the example, the GTP binding protein RAN (PDB: 1byu, chain A) was used. The gray, light blue, purple, green, blue and red chains were taken from 1byuB, 1a2kD, 1ibrB, 1k5gKL and 1l1mB, respectively (the four letter code indicates the PDB ID and the fifth letter means the chain ID).
Figure 2.
Figure 2.
An example of a PiSite entry. See the main text for details.
See this image and copyright information in PMC

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Publication types

MeSH terms

Substances

  NODES
3d 2
HOME 2
iOS 2
Javascript 1
mac 1
os 12
text 14
twitter 2
visual 2
web 7