CADD

10:54 PG | Posted by Iris

Its my third assignment, sharing what I've learned so far in CADD class.

1. MEROPS Database


Protein sequence
It provides catalogue and structure-based classification of peptidase. This is a large group of proteins that is important in medicine and biotechnology. MEROPS is a database of peptidases that are calssified into families and and then group into clans.In the class we select randomly some protein sequence and use BLAST from NCBI web to identify the similarity between them by having percentage (100% means it is similar). Besides, we can get their ID number.

2. PROTEIN DATA BANK (PDB)

PDB website

The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.


2. ARTEMIS software


Artemis sequence

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.

3. CLUSTALX

Loaded clp n lon sequence


To align multiple sequences and using Tree View to know their hierarchial view of information. Then, we can get their phylogenetics, the evolutionaryrelationship among variuos organisms.

4. RASWIN

1RR9 via Raswin


This is a software again people, even though sounds like Aswin right..huhu..just kidding..it can be used to view 3D structure of the protein (early in gz file, u have to convert it to pdb file in PDB web)....very cool when we can 'play' with the colour, rotate it 360..

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