Small Disulphide-bonded Proteins (SDPs) are a special
class of proteins that are relatively small in size (length <=100
a.a.) and have disulphide bonds within their 3D structures. SDPs
include many secretory proteins which serve predatory, defensive
or regulatory roles (such as toxins, inhibitors and hormones) and
they are rich source for therapeutic drugs.
SDPs have distinct properties from medium and large
globular proteins. They usually do not have a compact hydrophobic
core, which stabilize the protein structure. Their side chains are
more likely to be exposed to solvent and their conformations are
more flexible. The 3D structures of small proteins are usually dominated
by disulphide bridges, metal or ligand and tend to bind or interact
with large molecule. In small disulphide-rich proteins, the effects
of disulphide bridges and constrained residues such as prolines
are more significant than sequence similarity. As such, the comparative
modeling rules for such proteins are highly specific and different
from that of large globular proteins. These distinct features require
specific methods and datasets to be developed for the comparative
modeling of SDPs.
SDPMOD provides an automated comparative modeling
service to the research community. For advanced users, SDPMOD offers
a manual mode that allows for the selection of the desired template
as well as a semi-automated mode that allows users to select the
template from a suggested list. Besides the selection of templates,
advanced users can edit the target-template alignment thus allowing
further customization of the modeling process. Using these web services,
users can obtain models built using a workflow dedicated for comparative
modeling of SDPs using MODELLER.
Furthermore, the web service provides model stereochemical quality
evaluation using PROCHECK.
SDPMOD is freely accessible for academic or non-profit users.
In citing SDPMOD please refer to:
Lesheng Kong, Bernett Teck Kwong Lee, Joo Chuan Tong, Tin Wee Tan,
Shoba Ranganathan, (2004). SDPMOD: an automated comparative modeling
server for small disulphide-bonded proteins. Nucleic Acids Research,
SDPMOD server is proudly brought to you by
Lesheng Kong, Bernett Teck Kwong Lee, Joo Chuan Tong, Tin Wee Tan and