Computer Aided drug design

CADD Learning Software(s)

-Protein Sequence (MEROPS database)

First class of CADD was the introduction to protein sequence. The protein sequece can be taken form MEROPS online data base.

From this database the we can choose the protein sequence of preferable microrganism. Peptidase or Inhibitor can be search by by name. In this class we take the sequence for Lon and ClpP. 5 from each seguence were click and saved in the notpad. Next we identify the merops Id , name of the machnism , peptidase unit, active site and protein sequences.

-Clustelx


In ClustalX, we were taught on how to load the sequences. After loading all the sequences by clicking on 'file' then load sequence, we were told to do complete alignment by clicking on 'alignment'. Then, 2 files will be saved which are .dnd and .aln files.




- NCBI Blast




we were asked to go to NCBI to BLAST for pdb data. This can be done by changing the database under Choose Search Set category into Protein Data Bank proteins. Others will be the same as before. The sequences used in this class was from Burkholderia pseudomallei. After we got the description, we can see that in front of the description is the pdb ID such as 1TYF and 1RR9.





-Protein Data Bank (PDB)





The protein Data Bank archive is the single worldwide repository of information about 3D structures of large biological molecules. It provides information about structure, functions and others related to the protein.

In order to retrieve the information, we have to search for its pdb ID. As we typed in 1TYF in the search box, a page will appear about the protein. We were then asked to save the PDB fille and FASTA sequence. The same thing was done for ClpP with PDB ID 1RR9.

1RR9

-Atremis



Is the software that woks as genome viwer similarly a tool that can sho characteristic of the genome. This software can visualized the sequence features.










- RASWIN/Rasmol software

This software has a function in viewing the molecular structures of organisms. The viewing is in 3D that is result in more attractive view and understandable

1TYF structure

Journey of my life

BismilLAHhirRahmanirRaheem

Asslamualaikum,


I start my very first post with BismilLAhhirRahmanirRaheem. If not because of I'm taking Computer Aid Drug Design and the lacturer asks us to creat a blog. I'm not sure when I will have my own account. AlhamulilLah, I have it now and begin it with introduce myself to everyone. the journey of my life!! I was born when my dad and mom still doing their degree oversea away from home as a second child. I was just 5 months old when they completed their study and moved back to Satun, Thailand, where my home is. I spent the whole of my childhood at my place and finished my high school there.

Than, I came to Malaysia with hope that it will be better than my country in term of Islamic Environment. Because of I'm a foreign student so IIUM is my choice. I choose to do biomedical science for my degree and I'm now at my forth year. Almost done here,Yea Yea! To complete my degree at IIUM, I have to move 3 times to 3 states of Malaysia. First, Kedah in early 2005. I'm Albukhry scholarship holder which were required to do their English Presessional class at Albukhary complex at Kedah. Late of 2005, due to a renovation of the complex we have to move back to IIUM Gambak. Whan I entered to Kulliayah of science, we was asked to move to another campus "Kuantan" in year 2006. Now I'm in my final year in Clinical and Phamaceutical Research concentration. And what's next?. This is a question that I'have been asking myself these days and waiting for the answer..

That's all for now and I will update my blog soon with the summary of my FYP. Insha Allah