Tuesday, January 19, 2010

Today, I would like to share to all of you the knowledge I got from Computer Aided Drug Design (CADD). Till now, I already learned some bioinformatics tools for instance Merops, ClustalX and BLAST. Protein Database and NCBI websites are very useful to learn the basic steps of CADD. Actually, CADD is one of the branches of bioinformatics. As information, bioinformatics is the application of information technology and computer science to the field of molecular biology. Bioinformatics tools are the powerful software that may aid us to apply on those prospects.

So, let’s start our journey of CADD..
Firstly, we have to know how to obtain the protein’s sequence of desired microorganism. We have to apply MEROPS which is a peptidase databases which enable us to find out the protein (amino acid) sequences, its active site and its domain. In order to get the similarity of the sequences or highly conserved sequences with other peptidase, BLAST will do it for you.



On the further step, we can align the used sequence using ClustalX which can be viewed in TreeView. By aligning the sequence, we can have classification, hierarchy and phylogeny of the organism.

After that, let’s get to know about Artemis. What is Artemis? It is a genome viewer and annotation tool that allows visualization of sequence features and the results of analysis within the context of the sequence, and its six-frame translation.
At last, we able to view the sequence in 3D form by using Rasmol/Raswin.