Bioinformatics is an application of information technology and computer science to the field of molecular biology. Compared to its earlier applications, it is now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Taking Computer Aided Drug Design taught me the importance of bioinformatics. Among the common activities in bioinformatics are mapping and analyzing DNA and protein sequences; aligning different DNA and protein sequences to compare them; and creating and viewing 3-D models of protein structures.
We need a protein sequence in order to create and view the 3-D models of protein structures. Thus, to know the protein sequence we can find it through MEROPS, a database which provides information for peptidases/ proteases and the proteins that inhibit them. The peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism on the MEROPS summary page. The MEROPS database uses a hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan.
To illustrate, we can search for a peptidase or inhibitor by name. For instance, a peptidase which begin with ClpP.
From the information, we can get the peptidase unit (e.g: 1-73); active site of the enzyme (e.g: H(3) D(52)); and protein sequences in FastA format.
In addition, ClustaX software can be used in phylogenetics study, in which we can cluster and align conserved regions. Sequences are aligned using ClustaX and viewed via Treeview software. ClustaX helps in clustering organism by similarity, for example, organism under the same genus such as Burkholderia sp. whereas Treeview software allows us to display phylogenetic trees of an organism.
We learn to utilize BLAST (Basic Local Alignment Search Tool) program to compare protein or DNA sequence queries to protein or DNA sequence databases. BLAST is a collection of searching programs for biological sequence databases which uses the algorithm. For instance, in the BLAST NCBI (National Center for Biotechnology Information) BLAST page, we can search for protein database using protein query from “Protein Blast” program.
Once we enter the FastA sequence, and select PSI-BLAST (Position-Specific Iterated BLAST) as the algorithm program selection, we manage to get the domain, identity and description of the query protein sequence.
Next, we can find the location of the protein sequence in the genome using software known as ARTEMIS.
RCSB (Research Collaboratory for Structural Bioinformatics) Protein Data Bank (PDB) is an archive that contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. To view 3-D model of protein structure, we can use PDB identification number (PDB id.) such as 1TYF for organism Burkholderia pseudomallei.
The PDB file is downloaded from RCSB PDB and opened via software called RASWIN which consists of RasMol. RasMol is molecular visualization software which makes the 3-D display more interactive and interesting to be explored.
Alhamdulillah, these are the knowledge I gained during the classes and through readings. Even though I may lack on some information, but I found out that this subject is quite interesting. It’s true that it is challenging and difficult, but, I believe that my friends and I tried our best to understand whatever we learn in this subject….~ There is no elevator to success. You have to take the stairs. ~ unknown
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