About SDPMOD: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: SDPMOD Team:SDPMOD server is proudly brought to you by |