Assalamu’alaikum my dear readers.
How are you feeling? It has been a while since I last updated this page. Well I am an avid reader not a keen writer.
In our last class of Computer-Aided Drug Design, we were assigned with a task to explain what we learned and how much we understood from all those software.
Okay here goes.
Since we had no basic what-so-ever in CADD, our lecturer decided to teach briefly about Bioinformatics. In the first class, we were taught in sequence analysis by using NCBI and MEROPs is used to search organisms name based on its peptidase (ClpP and Lon). We were asked to find any random 5 organisms for each type of peptidase and paste it in worksheet.
Unfortunately, due to my sitting position I heard it wrongly and I thought it was only 5 organisms for both peptidases. The table comprised of organism name, protein sequences, peptidase unit, active sites and its MEROPs ID.
Then using BLAST, we were taught to find its function, percentage identity and sequence. All needed to be done was copy and paste the protein sequence in Protein BLAST then choose PHI-BLAST.
Consequently, for the second class we were taught on how to use 2 programs namely ClustalX and Artemis. ClustalX is used in Phylogenetic while Artemis for genome sequence which can be found in SANGER website.
In ClustalX there are 2 outputs that can be obtained. Firstly, it can gives alignment of different microorganisms while another function is cluster tree or TREEVIEW. Basically TREEVIEW is utilized in observing the clustering of microorganisms into same or singular branch (the relationship between the microbes).
Single cluster denotes no similar branch with the microorganism, only one and it has no similarity in sequence and highly conserved. For multiple clusters, it denotes that some microbes are in the same branch and have similarity in sequence.
To practice, we were asked to do it using ClpP and Lon from the previous class.
For Artemis, the amino acid sequences were copied from the same notepad (ClpP and LonA) then it was pasted in Navigator for ‘Find Amino Acid String’ column and ORFs in range was marked and unwanted sequence was deleted.
At the end of the class we were asked to find FASTA sequence of 1TYF using ‘Protein BLAST’ in protein data bank or pdb form.
Last but not least for last week lesson, we were told to use RasWin software using 1TYF.pdb file to view the protein structure in molecular level. There were many forms of presentation such as ribbon and ball and stick. Also there was multiple color representing the type of protein structure (alpha or beta-pleated sheet).
Then we advanced to introduction of CADD which comprised of calculation and equation which normally learned in Physics. There are Molecular Mechanics, Molecular Dynamic, Quantum Mechanics and Energy Minimization Theory.
Since I am quite slow in this part, I won’t explain it further. I guess that’s all.
C’est la vie~
