~CADD education~

Computer-Aided Drug Design (CADD) is 1 Credit Hour-subject that I have to take in this last semester of my final year degree. This entry also is one of the assignment which need to be done as a way to promote CADD...

CADD is one of the Bioinformatics study that use computational method to stimulate drug-receptor interactions. Bioinformatics is the application of information technology and computer science in the field of Molecular Biology. Basically, it deals with analyzing, mapping, aligning and viewing 3-D protein sequences and stuctures. There are seven areas of bioinformatics that support CADD; Virtual High-Throughput Screening (vHTS), Sequence Analysis, homology modelling, similarity searches, drug lead optimization, physicochemical modelling and drug bioavailability and bioactivity.

In first class, I have been thought on searching the protein sequence of organism with ClpP and Lon A peptidase by using MEROPS...Next, similarity searches of that protein sequence and analysis is done by using BLAST...In BLAST, function of the sequence can be identified based on domain and its similarity with other organism can be known by the descriptions.MEROPS will show the peptidase that we want;

BLAST output will show you this window;


In second class, I learned on clustering using ClustalX. Clustering also known as phylogenomics. In ClustalX, known sequence can be clustered together. The clustered sequences will show more nods when they are more similar to each other in the alignment view. The view clustering genomes via Treeview will looks like this;

Besides, I learned the ARTEMIS to know the required sequences in a genome. For example, I copy and paste some of the ClpP sequence with the Lon sequence, to create a genome. Then, this ARTEMIS will provide me the location of those sequences.


In third class, I have been thought on the 3-D view of the BLAST in the Protein Data Bank (.pdb file) using RASWIN software...


All these software need to be learned from the experties theoretically and practically as its very complicated to be understood...The picture below is the example of 3D output view of RASWIN;




Theoretically,the calculation and equation on protein modelling classified into five topics;
1)Molecular mechanics
2)Molecular dynamics
3)Quantum mechanics
4)Energy minimization
5)Molecular Calculation

I love to learn CADD very much and hope that this subject will help me in my future career=)

~Life continues, Allah's bless is my highest inspiration~