Smile =) or not...

Assalamu'alaikum all..

I think by now people would bound to notice that my posts seem to consist of my assignments. What to do. As much as I like to write I love reading more. Wee!!!

Oh we learned a bit on XML stuff today. Basically, it is a bit like HTML just that it has different command. We also learned PDB and SMILES.

Today I'll be showing another set of ChemSketch design. Well, apparently our mischievous acts in class was caught by madam (dang! kidding.. oh I love to be dramatic. :p) and she asked to do tutorial on SMILES. xD

They are the cute aliphatic and aromatic rings. Tell you what. The last time I did anything on organic chemistry was on my matriculation days. Probably have to scavenge the text from my room. Heh. Check it out.



That's all for now. Tata! :)

ChemSketch

Assalamu'alaikum. Today in KOS 1110 we learned how to manage ChemSketch. Believe me when I say it was causing me headache. UGH!
By the end of the class I was positively engulf in what could only be say prelude of a migraine episode.

Yeah I realized that my drawing is not on par with any architecture design or any art student for that matter. Boohoo..

By the way we were told to design a few diagram of:

1.Energy



2. Orbital



3. Vacuum Distillation Apparatus



4. DNA



5. Lipid


I'll be updating this entry if I ever got around it to explain how did we manage to survive this.

Till then.. I want to nurse my headache. Oh the joy. So not.

Journey of Life Part II

Assalamu'alaikum all..

It's been a long time since I last posted anything on my blog.
I'm in my final semester now. Lots of things had happened.
I've finished writing my thesis, submitted it and graded.
I went to umrah a week after my hard cover submission.
Went through couples of wedding of my relatives, funeral of my uncle.

Recently, my dad passed away. It's been more than a week. 10 days to be exact.
At first the sadness was overwhelming that I couldn't speak without tearing up. Gradually, I got better. I must accept that Allah loves him more than the rest of us.
Also, I wouldn't want him to feel tortured over my grieving. I love him too much for that.

He's my teacher, my troubleshooter, my partner in all my hobbies. We love the same things. Even my passion in photography was incited by him. All left now is memory.
Of him, of us. I hope that one day I could be strong when I think of him.

He's the best dad I could ever ask. He told me that life must goes on no matter what.
The living keeps on living while the dead will remain so.
I want to walk the talk. To show that I listen to him well and that I never want to disappoint him. That's what he likes best. As he always says, "Listen and be obedient."

I guess that is all for my first post.
Al-Fatihah for him. May he obtains Jannah. Love you dad.


This is one of my snaps. Yeah. I'm an amateur.

Lessons

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~