Treasures of CADD

Monday, January 11, 2010

On previous lecture of CADD, madam had asked us to post in blog about CADD, assuming that the visitors have zero knowledge about CADD. In other words, we have to review what we have learnt for about 3 weeks lecture..huhu. It’s quite hard for me bcoz I’m also still adapting myself with this new knowledge, CADD. Hopefully, I can recall some…By the way, CADD (Computer Aided Drug Design (CADD) is a specialized discipline that uses computational methods to simulate drug-receptor interactions. Now, lets review what had been learnt


1. we learnt how to get the protein sequence from different organism. This can be performed from website of MEROPS, search based on domain. Detection of domain is important towards the it’s function.The examples of domain are Clpp and Lon. Once the organism being chosen, the protein sequence will be appeared. From the protein sequence, we can get the peptidase unit and the active site.

example of Lon peptidase sequence for MER060788

2.Then, move to website of National Centre of BioInformatics (NCBI)

NCBI::::> Sequence analysis::::>Protein Blast::::>BlastP

-fill the blank with protein sequence of organism
- click non redundant on database
- then click psi.blast before clicking BLAST

From the blast, we can get the domain, description and identity. Description and identity can be found on the allignment. Identity means that how much the similarity. In short, we do BLAST to search the similarity.



On 2nd week, Clustalx and Artemis had been used. Clustalx is meant for clustering all those protein sequences while Artemis is a sequence viewer and annotation tool.

1.Clustalx software
a.Wordwrap sequence in notepad
b. Clustalx:::>file:::>load sequence:::>choose sequence from file

complete alignment in order to aligned all the respective sequence.

≈ output : dnd (dendogram)…………..need TREEVIEW to view
aln (align all the sequence)………..can b viewed by micr.word also

~ Treeview is used to view the hierarcy of organism

2. Alignment:::>complete alignment:::> align
3. Website MEROPS:>organism:::>eg. Bulkholderia pseudomallei

-choose SJ –S16 (*SJ – clan, S16- family)…for Lon
-copy sequence in notepad
-repeat procedure for SK-S14…….for Clpp

4. Artemis v5:::>file::>open:::>BPs.dbs:::>choose certain sequence from notepad clpplonbp

~ Go to:::>navigator:::>paste that certain sequence in blank at find aa string
~ create:::>mark ORF in range
~ output appeared 3 sequence …..delete sequences without similarity

1 feature left: edit:::>trim selected feature to met

5.To find another sequence which may have similarity within the previous sequence

a) repeat all in step 4
b)CDS:::>edit::>edit selected feature:::>copy name from notepad eg. MER165606
c)paste and replace “none”…apply…ok

6. Website NCBI

a)BLAST:::>protein blast:::>copy paste sequence:::>choose database : pdb
b)Alignment 1st line: 1TYFA (* 1TYFA – ID of pdB):::>Open 1TYF

7. open website Protein Data Bank::::>search IRR9:::>download file:::>save FASTA, save pdb


PDB is for homology modeling where the amino acid sequence of a specific protein (target) is known, and the 3-D structures of proteins related to the target (templates) are known.

Eg . Clpp …..1TYF.pdb

Open file with RasWin…..~output: 3D structure
3D structure info: eg. Green color: helix, Yellow color: B-shape (straight)

only until here I can recall...plz correct me if there is mistake..

Unit trust

Saturday, January 2, 2010

Tahukah anda?

Anda boleh memaksimumkan wang KWSP anda melalui pelaburan dalam unit trust? Pulangan KWSP tahun lepas hanya 5%. Tapi pulangan unit trust tahun lepas ada yang mencecah 33%. Oleh itu jangan lepaskan peluang ini. Bahkan anda juga boleh membuat pelaburan dalam unit trust dengan nilai pelaburan permulaan yang rendah

# Jika anda melabur = RM2,000 >>> Untung = 20% setahun, dalam masa 20 tahun, duit pelaburan RM2,000 anda akan menjadi = RM2,000 x (1 + 20%)20 = RM76,675.20 SUNGGUH LUMAYAN!!

# Jumlah kos pengajian degree di IPTA = RM 25,000 manakala kadar inflasi semasa = 3.5%. Katakan anda mempunyai anak berumur 2 tahun, dlm masa 15 tahun lagi dia akan melanjutkan pelajaran ke IPTA..! Jumlah kos pengajian degree di IPTA tahun 2022 = RM25,000.00 x (1 + 0.035)^15 = RM41,883.70 Oleh itu, ELAKKAN masalah kewangan ini berlaku kepada diri anda kelak!...

Jika anda benar-benar ingin menikmati pulangan lumayan dari sistem penjanaan wang, inilah pelaburan yang sah disisi undang-undang malaysia. Mulakan pelaburan bijak anda dengan pelaburan unit trust.

Memandangkan kita da semakin dewasa, kita da kena pk suma ni tuk future..

Kawan2,jika nnt2 anda da keje or skrg pon kalo berminat tuk invest dalam UNIT TRUST PUBLIC MUTUAL ISLAMIC, sila2 lah contact sy x pandai nk promote secara suka face to face tuk explain psl unit trust ni...

Dulu sy hny tahu sedikit2 shj psl unit trust. tp bila sy da invest sendiri, sy mula belajar banyak benda tentang kewangan..secara x langsung juga kita menjadi lebih bijak dalam manage financial kita...

All about FYP

Sunday, December 13, 2009

My final year project titile is “Cytotoxicity activity study of Nauclea subdita leaves extract”. Generally, it is about the screening of Nauclea subdita leaves extract whether it has the possible anti cancer properties or not.

“ the roots, the barks, the leaves and the sap of Nauclea subdita had different useful parts for food, medicine, construction and commercial uses” - Murniati, et al.(2008).

This is why Nauclea subdita was chosen because it is rarely being investigated scientifically and too little information regarding of this. The keywords for this study is “genus Nauclea is known to produce many kinds of indole alkaloids”. One of the biological activities of indole alkaloids are antiproliferative (anti cancer).

There were 3 types of cells have been treated with N.subdita leaves extract …HSC3 oral cancer, H1299 lung cancer and HACAT normal cell. The results might be varies. .The extract might have anti cancer properties (selectivity inhibition) against different neoplastic (cancer) cells growth.

Until at this moment, the results have not been interpreted yet. Generally, we have to determine the IC50 from the graph. The graph must be created first from the result as a serial dilution was done for the treatment (extracts). In other words, we have to determine at what concentration of extracts that would inhibit 50% of cancer cells. If the IC50 is less than 30ug/ml, only then it will be considered to have anti cancer properties.

So, to madam or anyone who has any suggestion regarding of my topics, you are most welcomed. Your contribution is highly appreciated.

To all friends, best of luck for your FYP as well. May this FYP would benefit us a lot.

journey of my life

assalamualaikum to all....finally i have created my own blog as our lecturer, mdm noraslinda asked us to do is good actually for the person like me..huhu.thanks madam.frankly,this is my first trial in writing some sort of i am not good in all, i am sorry for my broken english.maybe with the presence of this blog, my english would be better.ok...let's proceed to the first task..."the journey of my life"...I am Suzaila bt Arsad from Trolak, Perak.

School attack

My primary school was Sekolah Kebangsaan Trolak Timur. Then, I went to Sekolah Raja perempuan Taayah, a girl’s religious boarding school at Ipoh. This was the first time where I was surrounded by multi backgrounds of friends. Truly, I felt very low self-esteemed because I was a village girl. The fluency of their english also scared me…huhu. First 2 years there, I was studied hard because I really determined to be placed in the first class (40 students will be selected). Haha..i can still remembered I was on 37th places among 160 students from final examination result. ..I got the top class in form2 but still I was among the lowest in the top class. Again, in form2 I was struggled to perform better because my places was not in a safe zone. Alhamdulillah, I was still in the same class on form3 with “belas2” places. But in form3, I was changed…I realized that I was not enjoyed in studying hard..I had promised to myself that I won't study hard anymore.. girl’s school…almost all of us must break the rules…like one of my friend here said “budak Taayah mmg nakal2.”

Then, I was offered to MRSM Jeli, Kelantan with the other 4 friends from Taayah. We had experienced so many punishment by wardens…drew mitosis and meiosis notes for each class, ran all over schools for 3 rounds, being caned 2 times by principal and many more. No punishment without no reason, right!But I really enjoyed every moment was among the precious memories that I wont forget. All teachers there were very supportive and so kind to us. Sometimes, we were like friends as well. Thanks to all my teachers for their kindness and helped me a lot in study.

The most important thing I had learnt from school's life: we should not be a very low self esteem person because we also can achieve like others. Also, I really thanks to my parents because they had sacrificed alot to me and my siblings.

He was gone forever

On 9th August 2008 at 5.45am at my sister’s home, we were surprised with the news from my mom…my dad was gone. At first, it’s hard for me to believe it because the thing that I really scared of already happened. But I believed that he was gone in a peace during his sleep and I never saw my dad’s face as calm as on his death.

We always kept thinking and gonna scared with the loss of our parents, but when the times comes, only then we will realize that we will never be prepared to face it even if we could know the exact time it will happen.

Now, I only have dreams to relief the feeling of miss to my late father and my late brother. I always pray that they will be rest in peace there.


Degree’s life

I don’t know what to tell here. Maybe I can recall better after graduating and leaving UIA…huhu. But I’m sure I’m gonna miss everything here soon especially friends. So, I just recall educational trip to Singapore was one of the best pleasures in my life. Alhamdulillah I was selected and I believed it was ‘rezeki’.

Now, only about 4 months left for us to face the real life and determine our own way. I am the person who has no specific ambition . Sometimes I am not so determined in my way. My aim is only that I want to be ‘SOMEONE’. I wish may happiness and success along with my way.

Clumsy things

I believed everyone had experienced lots of clumsy things in as well. But the clumsiest thing that I won’t forget was on last year. I was being left by bus at R&R gambang. At that critical moment, I couldn’t make the right decision. The only thing kept in my mind was only to safe my laptop which was in the bus. I had asked a lorry driver to help me as they also on the same way to KL. It seems like in a TV but now I already experienced it where I was in a lorry with 2 guys that I never knew them. But in the lorry, I was only could think deeply if they might do bad to me. ..I had just prayed hard that may Allah saves me. Alhamdulillah everything was safe.. I got my laptop n all my stuff from the bus.