Chemistry Reference
In-Depth Information
Table 9.6
Fragment of the
result of SH2 domain search
using 3DID server
PDB
Chains
1a07
A, B
1a08
A, B
1a1a
A, B
1a1b
A, B
1a1c
A, B
1a1e
A, B
1a81
A, C, E, G,
...
1ab2
A
1ad5
A, B
1aot
F
1aou
F
1a1a
A, B
3DID is a database of high-resolution three-dimensional structural templates for
domain-domain interactions. It contains templates for interactions between two glob-
ular domains as well as novel domain-peptide interactions (Mosca et al.
2013
).
Table
9.6
presents a fragment of the result obtained using 3DID server for the SH2
domain search, i.e. the PDB entries that contain the SH2 domain (the total is 285
structures).
Several other web servers for PPI prediction are: JENA PPI server (
http://www.
imb-jena.de/jcb/ppi/)
, meta-PPISP (http://pipe.scs.fsu.edu/meta-ppisp.html),
SPPIDER (
http://sppider.cchmc.org/)
, SNAPPI (http://www.compbio.dundee.ac.uk/
SNAPPI/inde9.jsp), hotPOINT (http://prism.ccbb.ku.edu.tr/hotpoint/), PINUP
(http://sparks.informatics.iupui.edu/PINUP/) and InterPreTS (http://www.russelllab.
org/cgi-bin/tools/interprets.pl).
9.6
Conclusion
This chapter summarizes and illustrates several on-line tools which are publicly
available in the context of protein surface analysis and comparison, protein-ligand
and protein-protein interactions respectively giving an overview of the most versatile
and efficient webservers. Web-based computational tools allow investigation and
comparison of protein sequences and structures, predictions and characterization of
their interactions with small molecules or other proteins. Integration of all these data
concerning protein sequences, structures and interactions permits to decipher the
mechanisms of cellular both physiological and generating diseases events.
