Agriculture Reference
In-Depth Information
Table 2.8
(continued)
Database Name
Plant Species/Purpose
Uniform Resource Locator
(URL)
CATH: Protein Structure
Classification Data-
base—Prof. Orengo's
Bioinfomatics Group at
UCL, London, UK
Proteins classified into struc-
tural domains and superfam-
ilies; useful web site once
protein identity is known
even with plants
SCOP: Structural Classifi-
cation of Proteins
Contains proteins in fold
domains and superfamilies;
useful in assessing protein
structural similarities across
species
PANTHER—Classifica-
tions of Genes and
Proteins
Browser and search engine
for proteins, and divides
them into ontogeny and
superfamilies
RIKEN (RSGI)
The RIKEN Structural Genomics/Proteomics Initiative (RSGI) in Japan is an im-
portant and key centre for structural genomic and proteomic analysis. BioLOD.org
is another of the RSGI sub-web sites for structural proteomics. The RIKEN SGPI
has solved over 2,700 protein structures, including 33 from Arabidopsis that appear
on another important web site, the PDB site listed below.
SBKB from PSI Nature
Keeps you informed about advances in structural biology and structural proteomics.
It is an easy to navigate web site and includes information on other proteomic re-
search done at other web addresses.
PSI and F1000
The Protein Structure Initiative (PSI) in the USA, and the structural genomics cen-
tres of Europe (Yokoyama et al. 2000) are important sites. The PSI has promoted
large-scale attempts to determine the 3D structure of proteins and deposition into a
database. In 2005, the PSI shifted to its second phase, known as PSI-2 'information
phase' which was to solve more challenging structures such as protein complexes
and folding, and to identify membrane associated proteins (Fox et al.
2008
).
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