Agriculture Reference
In-Depth Information
X-Ray Crystallography
X-ray crystallography has also been used to determine the protein structures of
almost 90 % of protein entries in the PDB database. The third generation X-ray syn-
chrotrons have become essential for macromolecular crystallography (MX) of large
proteins and protein complexes (Samatey et al.
2001
). For example, the synchrotron
SPring-8 of RIKEN in Japan has been used to determine the structures of important
membrane proteins and large complex proteins; such as Ca
2+
-ATPase, rhodopsin
and flagellin (Palczewski et al.
2000
; Samatey et al.
2001
; Toyoshima et al.
2003
).
InformationandWebResourcesinStructuralProteomics
Bioinformatics and related databases are therefore important tools for advancing
the study of structural proteomics. The methods used in computational prediction
of protein 3D structures are readily available and described by Zhang (
2008
) and
Zhang (
2009b
). Free modeling, which is sometimes called '
de novo
' modelling is
used to predict the 3D structure of proteins, and the web-based sites for information
on structural proteomics, their purpose and URL are detailed in Table
2.8
.
I-TASSER
A number of web servers and computational tools for free and/or template-based
protein modelling have recently been made available; for example, the I-TASSER
internet server.
CASP
I-TASSER is often used in Critical Assessment of Techniques for Protein Struc-
ture Prediction (CASP) (Zhang
2009a
). This template-based modelling method is a
comparatively new method for matching proteins using evolutionarily related pro-
teins of known structure as a template.
Swiss Model Server (DisEMBL)
There are many web services and tools (e.g. Swiss Institute of Bioinformatics
SWISS-MODEL server) to support template-based modelling (Schwede et al.
2003
). The Intrinsic Protein Disorder prediction program, which is linked to the
Swiss Model server, is one such piece of software.
Search WWH ::
Custom Search