Review for CADD

Computer Aided Drug Design(CADD), a specialized discipline that uses computational methods to simulate drug-receptor interactions classes. This post is to share some simple steps to view your protein in 3D version starting with the selection of specific protein sequence.

1. Search and retrieve protein sequence from different organism.
*go to "http://merops.sanger.ac.uk/" and click "searches" on the left bar and choose the first search button next to "by Name".

*key in "ClpP"(a specific protein domain) and press "enter".detection of domain is important to know its functions and similarities.
*choose S14.001 and click at its link.here you can see detailed profiles on that specific protein.
*click sequences link at the top.choose any of the organism with that specific protein and click at their specific protein type starting with MER****** and specific protein sequence will appear in new window.From the protein sequence, we can get the peptidase unit and the active site.
*copy and paste all the protein sequence in "notepad".Save as "ClpP" and then delete unnecessary information and save as "ClpP seq".
*repeat these steps for domain of "Lon" >> choose S16.001 for E.coli >> do same for other steps and save as "Lon" and "Lon seq".

2. Application of BLAST software to know the identity and description
*go to "http://www.ncbi.nlm.nih.gov/" and click "blast" in the box at the top right of the page and click protein blast

*Change only in program selection and click "blastp (protein-protein BLAST)"
*copy and paste your protein sequence and its code name from "ClpP seq" and "Lon seq" and paste it in query sequence box and press enter.choose psi.blast and click BLAST.
*choose the first line and note its identity and description of the protein in excel.Identity means that how much the similarity. In short, we do BLAST to search the similarity.

3. Application of ClustalX and Artemis software. Clustalx is meant for clustering all those protein sequences while Artemis is a sequence viewer and annotation tool.
*Wordwrap sequence in notepad
*Open ClustalX software--> file -->load sequence -->choose sequence from file "ClpP seq" or "lon seq"

the output for this software was in dnd (dendogram) which need TREEVIEW to view and
aln (align all the sequence) which can b viewed by micr.word.
*click at Alignment --> complete alignment --> align
*Go to Website MEROPS --> organism --> eg. Bulkholderia pseudomallei
*choose SJ –S16 (*SJ – clan, S16- family)and click on its link for Lon and copy sequence in notepad and repeat procedure for SK-S14 for Clpp
* use 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
*feature left: edit --> trim selected feature to met

Repeat previous steps to find another sequence which may have similarity within the previous sequence.
*click CDS >> edit selected feature >> copy name from notepad "MER******".
*paste >> replace "none" click "apply" and "ok"
*go to NCBI webpage again and click BLAST >> protein blast >> copy paste sequence(Lon and Clp each) >> choose database : pdb
*Alignment 1st line: 1TYFA (* 1TYFA – ID of pdB)>>Open "1TYF" for Clp
*go to "http://www.rcsb.org/pdb/home/home.do" >> search "IRR9" for Lon >> download file >> save FASTA, save pdb.

4. Application of Raswin software to view protein from pdb file in 3D model.
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.
e.g ClpP--> 1TYF.pdb
and Lon-->1RR9.pdb
*Open both of the files above with RasWin to have output in 3D structure with few information of their structure such as Green color: helix, Yellow color: B-shape (straight).

thats all for now..this is open for any correction from any of you..hope that i have helped you in some way..huhuuu
Wassalam

Remembrance of PrimaRy sChOoL LiFE~~

Bismillahirrahmanirrahim..
Assalamu'alaikum w.b.t to all my beloved friends and followers(if i hv any??)..

Now i would like to share some of my precious little memories that i hv hardly able to remember on my primary school days in Sekolah Kebangsaan Klang Gate(SKKG)..huhuu...
A very long loong time ago...at least i cud hv remembered that my school life is more fun than being at home..huhuu..i think i would list the stories by new lessons learn in life:

1- I can be unexpectedly clever when there's no challengers around me...

Since i was in standard 1 until 3, i was put in either the 1st or 2nd highest class in school..i could barely get to be in top 5 ranking during those 3 years(only once in standard 2 i get 2nd place)..when i was in standard 4, suddenly, a new "discrimination" system implimented in my school(without mentioning in particular the discrimination is about what)..i was thrown down from the 1st class to 5th or 6th class if i'm not mistaken (with less competitors for exam purpose i guess..wink2;p) due to the *discrimination reason...hurmm..it was really upsetting for me at first..however, i kind of enjoyed it...with less pressure from the competitors(classmates) and teachers(who doesn't expect much from their students), i managed to be in 1st place ranking in class in every examination for 2 years in a row..i only have 1 competitor in class which i really remembered...Nurul Sobah..huhuu...she is a very clever girl...there is one time i've heard that i got the highest mark among all standard 5 classes in a subject(i couldn't remember in particular which exam)..and then we got back into normal class distribution system in standard 6 for UPSR..and i got to be back in the 1st class again..huhuu..sadly, too much competitors lessen my ability to score well in examination(or is it just an excuse??;p)...coz i could barely be in top 5 ranking in the class during standard 6...however, Alhamdulillah I managed to get 5As in my UPSR..

2- i learn that sulking was a really bad and wasting habit..

huhu..during my standard 4 year, i got this one close friend of mine(whose also my competitor in exams) whom always sulk with me..i always become weirdly confused with her feelings and attitudes towards me at that time..however, because of my childish jealousy feelings with my one and only big brother during that time, i decided to try and test the sulking attitude with my family..but(cut it short) it seems like it didn't work..and i didn't really enjoyed it..hahaha;p..

3- i really was not interested in any love matters during my primary school..

i realized that i do have crushes on few boys during my primary school days but it was never serious..but one thing i realized during the time is that i could not be told if any boy do like me..huhuu.. i remembered once my friend told me that there was one friend of us (fellow prefects) like me and that particular information makes me have nightmares for few nights..and i was really afraid of bumping into him..thank god that he was transferred to another school not long after i knew that he likes me..hahahaa;p..since then i don't dare to talk on liking or not liking anyone in school..huhuhuu

4- i learn how to like mathematics very much..

i got this one particular math tutor which i went for tuition few nights per week..he was really good in teaching math and making his students score for the subject...but sumtimes this tutor(which is also a teacher in our school) can do unimaginable punishment to his student for being lazy or not able to answer his question..huhuuu...very scary "cekgu slemang"..uhuhuuu..however, i do love him very much as a teacher of mine and thanked him a lot for making me a clever math girl during that time..hahaha;p

In general, the whole experience that i've had during my primary school days was very beneficial for my growing up process in life...i really appreciate each and every moments i've had with my ex-primary schoolmates(which are/are not in contact with me now) and teachers..Jazakumullahukhairan kathira..insyaALLAH:)