Homology modelling Servers

 Swiss Model

Homology modeling of proteins involves four steps: template selection, target-template alignment, model building, and model evaluation. To achieve the 3D structure efficient computer programs are required. A huge gap between the protein structures and available protein sequences developed the need of automated, stable and reliable modelling methods . The idea of an internet based automated modelling facility with integrated expert knowledge was first implemented 10 years ago by Peitsch and co-workers and formed the starting point for the SWISS-MODEL server. Swiss model is reachable on World Wide Web.To get the Swiss Model results first step is to submit the amino acid sequence of protein whose 3D structure is not predicted yet. After submitting the amino acid sequence the BLAST search will be run against the sequences of known protein structures from the EXPDB which is the library of Swiss Model. After this procedure choose the three best models (target sequences) for the protein whose structure is not predicted yet. The 3D template is chosen on the basis of sequence identity with the target protein. For better results the sequence identity must be greater than 50%. Models having highest sequence similarity are chosen as template for our target protein. Download the target sequence for best three models in in PDB format. Swiss model provides you the four lettered code to find the template sequence for targets being chosen on the basis of sequence similarity. By entering this code in protein data bank (PDB) we will get the template protein sequences for the target.

CPH Server

CPH modeling server is a protein homology modeling tool. It is used for the 3D structure prediction of the target protein whose structure is not predicted yet. To find the template of our protein of interest first step is the submission of query sequence in the form of FATA format. For this purpose the sequence is pasted in the text field given.  After submitting sequence, the searching for the template is being done by BLAST and at the end website updates the results. In CPH the template recognition is based on profile profile alignment.

Hits are obtained from PDB using profile matrix that is generated by psi BLAST against a UNIPROT database. After the hits were in PDB data base, the PDB entry (4 lettered codes) and chain identifier are listed for the template to construct the three dimensional structure . The sequence identity is also given for the template of our target protein. The results from the CPH Model are given in the (Figure 2.1.2).

Besides accuracy the most important feature of the CPH models is its speed and it will give results in hardly 20 to 25 minutes.