Moments Frozen in Time

Since I have written my journey of life in the story telling which was about early of this year, you can see it here, I will resume the post with a continuation of the story.

Okay, since the last time I posted, I have continued my study in my 4th year, where I had taken a concentration course of clinical and pharmaceutical research. This course concentrates on the design of drugs and its application in the field of clinical and pharmaceutical medicine. It was very interesting learning the drugs, the drug design as well as its application in the world of science. Apart from that, there are also classes on research methodology where we learn how to create a proposal for the final year project. I have also taken CADD class with Mdm Noraslinda, where we learn how to create drugs using various computer programmes. I have also taken up a final year project where I did on the toxicity testing of the compound called 'Sapium baccatum'.  It was a fascinating and interesting task. It is to my belief that I have managed to accomplish the initial objectives of my final year project. Now I am currently taking two courses in this semester which are LE4300K (English for Occupational Purposes) and KOS1110 (Computer in Science), in which I hope I would do well, insyallah.

I had also went to both Makkah and Madinah during my one-month vacation. It was an interesting visit and alhamdulillah, I have managed to perform Umrah several times. Below is a picture taken on a visit to one of the museums there. : D

Steps in achieving protein 3D in CADD

1. Firstly, get protein sequences from MEROPS database (merops.sanger.ac.uk).

a. Once you open the main website, click on searches and search for ClpP.
b. From there, click on S14.001 and then, click sequences.
c. Click on the link with MERXXXXXX and the window will show the protein sequences for that merop ID.
d. Copy the whole protein sequences from >MERXXXXXX until the end of the sequences. An example would be such as this:

>MERXXXXXX - peptidase Clp (type 1) [S14.001] peptidase unit: X-X ( active site residue(s): X,X ) (Burkholderia cenocepacia) (Source: ProtID)
X MIHQPLGGARSQASYIEIQASEIVYLKERLSCLLAQYRPQEVKSIARDTDRDNFMSSEDA XX
XX KAYGLIDQVLLKRP XX

2. Make a table based on the information that has been obtained according to these criteria:

a. Merops ID (which is the MERXXXXXX)
b. Organism (the name of the organism)
c. Peptidase Unit (PU) (which can be obtained through the data obtained earlier)
d. Active Site (AS) (also from the data earlier)
e. Protein Sequence (the part where the sequences are – you have to delete everything, leaving just the sequences) The above data would become like this:

MIHQPLGGARSQASYIEIQASEIVYLKERLSCLLAQYRPQEVKSIARDTDRDNFMSSEDAKAYGLIDQVLLKRP

3. After finishing, open the website for NCBI (ncbi.nlm.nih.gov). From here, FASTA sequences must be form in order to do protein blast. FASTA sequence is protein sequence with merops ID. It should be like this:

>MERXXXXXX
MIHQPLGGARSQASYIEIQASEIVYLKERLSCLLAQYRPQEVKSIARDTDRDNFMSSEDAKAYGLIDQVLLKRP

PS: Save it in a notepad file

4. Once you’ve done it, click on the blast link which will bring you the blast site and then, click protein blast.

a. Copy and paste the FASTA sequence into the box, and if you did it right, when you click on the empty space of the job title, the merops ID will emerge.
b. Under program selection, click on psi-blast.
c. And then click on BLAST.
d. When everything is loaded into the new window, click on the first line of the alignment scores, and you will be able to observe its function and identities %.

5. Do this a few times with other protein sequences. Save the one with the FASTA sequences all in one notepad.

6. Now, to do ClustalX. The function of ClustalX is to do protein alignment. In order to do ClustalX, you need to have a notepad file with the FASTA sequences.

a. Once you have the file, click on clustal.exe icon and then click on file, and load sequences. Open the FASTA sequence file.
b. Once all the sequence are inside the ClustalX, click on alignment and do complete alignment. Click on align.
c. There will be two new files that was created with the same name but different format. It should be .dnd and .aln.

7. To do Artemis (a DNA sequence viewer) , first you have to search for another organism, which is Burkholderia pseudomallei. Get the protein sequences of ClpP and Lon-A of the organism.

a. Go to Merops website, click on organism and click B, to search for B. pseudomallei. Click on the link.
b. Then, for Lon-A search the site for clan: SJ and family: S16. Click on its merops number. (MERXXXXXX)
c. A pop up will emerge showing its protein sequence. Copy the sequences into a notepad. Do the same as you did the ones from before, which means form the FASTA sequence.
d. Now, do the same for ClpP, which can be found at clan: SK and family: S14.001. Click on its MERXXXXXX

8. Now, click on the artemis_v5.jar.

a. Go to File > Open and select BPS.dbs file.
b. Click Goto and then Navigator. Copy a portion of the protein sequence from Lon-A peptidase and paste it into the ‘Find Amino Acid Strings’. And click Goto. Do the same as ClpP sequence.

9. Next, would be the formation of protein 3D using RasWin programme.

a. Firstly, open RCSB protein data bank and search for Lon-A. Search 1RR9 through the list (page 2) and download a pdb file (it is the first icon under the 1RR9).
b. Then, after saving the file, open RasWin programme.
c. The only thing to do then is to open the file with the RasWin programme.

Thank you for reading. Forgive me for any shortcomings of this post. Hopefully this would help you in understanding CADD class.

Let’s see…

I have first started my education at a small nursery in Kuala Lumpur which was called Ladybug Kindergarten. Not much could be remember there as the only memory that I could recall is being sent early in the morning and picked up by my mom at the end of the day. Later, when I was 5 years old, my father got stationed at Sarawak and thus, we have to move to Kuching for a while. I have continued my early education at Sinaran Kindergarten there. I guess there is not much to talk about my kindergarten days.

Anyway, for my primary school, I was enrolled in SRK Ong Tiang Swee where the majority of the students are Chinese but the teachers mostly teach us in Malay or English. I’ve studied there for two years and in the middle of standard two, my father was stationed back to Kuala Lumpur, thus, having to move again, leaving my friends behind. Then, I continued primary school to a school near my residential area, SK Wangsa Melawati. It was a bit awkward at first, as I basically did not know anyone in there, and I thought that most of them basically knew each other already. Being the new kid at school felt odd, but the teachers tried to assist on making me feel like I’ve been there already. I made a few friends and at the end of the year, I have achieved quite amazing results. Later, in the next year, I was elected as a prefect of the school as well as the assistant monitor. Apart from that, my friends and I managed to represent the school in a district competition and came out as the winner of the competition. It was one of few precious moments of my life. My study went great at the school, and I managed to skip a class which ended my primary school education, a year earlier than expected.

Apart from studying at SK Wangsa Melawati, my parents also enrolled me into a religious school near my house where I spent most of my evening time, studying all the religious subjects. I did not excel well in my religious studies basically because I am mostly asleep all the time. Due to my skipping a year in my primary school, I also have to skip a year in my religious which is a not so good thing, since I missed a lot and there was too much to learn in such little time. In the end, I’ve managed to get a passing grade for my IMPORTANT examination.

In year 2000, my secondary education continued as I enrolled into the school next to my primary school, SMK Wangsa Melawati. For the first three years of my study there, I was an active student, as I participated in some of the sport events as well as represented the school in a few marching competitions. Participating in these events was really fun and gave a valuable experience as I become more confident as well as gain more friends. One of the few memories that I really could remember of this school was one where I was slightly injured in a small lab incident. It was something that I had never expected to happen but none the less, it happened.

Anyway, in my fourth year of the school, I was offered in place in one of MRSM institution, in which I went with a very heavy heart. With this heavy heart, I hardly could focus much and felt really homesick, thus, I quit the school in just a week. I guess that could be a record for me… hmmmm… Later on, I enrolled in SMK Aminuddin Baki, where I was placed with students taking Pure Sciences course with me. In most of the subjects taught in these two last year of secondary school, I’ve excelled the most in Additional Math and Modern Math subjects. I graduated from this school with flying colours and with my SPM results in hand; I applied for a place in the Matriculation Centre of IIUM.

I was first offered Physical Science but I changed my course to Biological Science because I am more interested in studying courses such as molecular biology and genetic at that point. I did well, but not really exceptionally well, as I graduated from my matriculation centre after one and a half year studying there. Studying at the matriculation centre was a really educational experience and I’ve met a lot of people there. I once had a roommate whose parents are currently staying at Mesir and she brought me back a cute camel doll which when you squeezed the middle of the stomach, an Arabic song will come out. I also met a lot of other students coming from other states in Malaysia, and it was really an eye-opener for a girl who never been out much except for small family vacation which is rare.

Later, I continued my study here in Kuantan Campus. Not as I expected, as we were first informed that we would be studying in Gombak in the first place before we were yet again informed of the change. But I guess, we should see things positively. Since the year 2006, I have studied and learned a lot from our respective lecturer, and by learning, that also means learning how to expect what kind of questions and what type of lecture the lecturers would give. My first year of study went through roughly because basically I was new to the process of learning in the university and also a bit awed by the prospect of being in the university. Later on, to the second and third year of my study in IIUM Kuantan Campus, I managed to understand the process and tried to grasp the learning procedure in the campus.

In this year, during the short semester break, I have managed to complete my industrial training at Hospital Kuala Lumpur which is always a busy place to be. However, there are times I wished I could have applied somewhere else due to the overcrowding of other students coming from other universities but nevertheless, I highly appreciate the skills and knowledge that we received during our working there.

Now here I am, writing this post and waiting for other ideas to burst out from my mind, so that I may I continue writing this blog…

Assalamualaikum and a very good day to my first time readers....

I'm Farah Dayana Ishak and currently 21 years old. This blog is to share with you my happy, sad and even golden moments in my life since I was a child till now. Hopefully, I will be able to continue this blog even in the future. Anyway, any suggestion or good comments regarding my post is highly appreciated but those with hurtful words will be ignored immediately.

Let's get to the first and foremost topic yet.... ME!!

Again, my name is Farah Dayana Ishak and I am 21 years old. My birthday is on 14th May 1988 and I was born at Hospital Kuala Lumpur at 10:06 pm... if I am not wrong. My blood is AB positive, and regardless of what people might think, I am not stingy.... hmmmm... I am from a family of four, with my ever loving parents and my younger sister. My dad is a military officer while my mom is a full time housewife. My younger sister is currently pursuing a medical education at CUCMS.

I am slightly talkative, but sometime shy around people I don't know. Usually, I am slow in taking the initiative step on knowing other people, due to the shyness. But once I know them, I can talk continuously with others. I am also a slight pessimist person because I usually see the bad before the good. I also like buying odd stuff, things that some people produced that are different from what they are usually. I guess in a way, it's my hobby, which also include reading fantasy and futuristic novels.

Little things in life is what makes us appreciate it better... ;-)