lets learn CADD

Posted on Saturday, January 9, 2010 by shazwani


CADD or in its full and long name called as computer aided drug design. 1 credit hour subject that i have to take in this final sem otherwise i cant graduate..hahaha..very huge impact..

The course was tought by a very beautiful and nice lecturer, Mdm Norhaslinda.. this course is subjected to the aplication on computational methods where the knowledge can be applied in designing drug..

in the first class i learned about how to search for protein sequence from MEROPS, the peptidase database.
The summary page describing a given peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism. The Summary describes the classification and nomenclature of the peptidase and offers links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these again have indexes. Each of the Summary pages offers links to supplementary pages.

For instance domain peptidase for CLPP and Lon. the sequence is very unique to a particular organism and present with its own merops id number. for example MER12345..once the number is clicked,it will pop out the respective sequence for the domain chosen before and also a description related to the protein sequence..

example of Lon peptidase sequence for MER060788


next, we need to blast the sequence on the ncbi website.
Open NCBI website and click Blast. Go to protein blast and blastp. Copy the Merops ID of Lon with the sequence from the notepad to the box. Choose for Protein Databank protein (pdb)

after that, click blast and it will give the band sequence of the organism. the first red sequence shows the highest similarity to the data sequence from the data bank.

8.


next class, i learned about CLustalX and artemis, also protein blast from protein data bank. ClustalX is a software where several peptidase sequences are clustered and aligned together. the peptidase sequences are obtained from the merops website earlier.

open the clustalX folder and then loaded the sequences..next click do complete alignment in order to aligned all the respective sequence.
the sequences will be aligned according to the similar nucleotide sequence for the different organism.

aligned sequnces of several organisms

Clustalx also enable us to view the hierarchy of the organism by the Tree view option.


artemis is a software that can be used to visualized sequence features andthe results of analyses within the context of the sequence, and its six-frame translation. In order to view the sequence, Artemis requires Java software.




The BLAST from pdb file can be use to analyze similar 3d structure. the 3d structure can be viewed with another software name RasWin..from this software,we are able to view several modification to the 3d structure such as structure of ribbon,temperature of the molecule and it gave different color for different atom and chain or bonding.


3D view from RasWin software



i hope you guys can get a general view and benefited from it..i'll keep update this entry if there smthing i need to add up later on..

1 comments:

Noraslinda says:

Salam...

Thank you...