Lets learn Computer Aided Drug Design or CADD... Basically we must have basic knowledge of bioinformatic tools ans Protein Data Bank...

Bioinformatic tools provide software that helps researchers to find sequence and classify unknown organism.... Normally in molecular biology...This tools can save the cost and times..

A) MEROPS - Provide database of peptidase in organism.
Website: http://merops.sanger.ac.uk/

  1. SEARCHES --> Search by Name
  • By searching based on certain peptidase such as Lon or ClpP, protein sequence of certain organism was obtained. It also provides peptidase unit and active site.

B) BLAST (Basic Local Alignment Search Tool) : Provide similarity in sequence of organism. Website: http://blast.ncbi.nlm.nih.gov/Blast.cgi

  1. protein blast --> blastp
  2. Enter Query Sequence (FASTA sequence) --> Job Tittle
  3. Click Non redundant Protein Sequence on and Select PSI-BLAST
  4. Click BLAST
  • By searching database using non redundant protein sequence using PSI-BLAST, the similarity of organism can be known through its domain, identity and description.

C) Clustalx (Multiple Sequence Alignment) - Clustering or align multiple protein or nucleotide sequence. Software can be downloaded from www.clustal.org/ . This software need JAVA.

  1. Go to Clustalx.exe file
  2. File --> Load Sequence --> Choose notepad file that have protein sequence
  3. Alignment --> Complete alignment --> Align
  • Two output file will be produced from this alignment which are dnd file and aln file.

D) TREEVIEW sofware - Display phylogenies of organism

  • Output file is viewed through TREEVIEW Software. If not, it also can viewd through Microsoft Word

E) Protein Data Bank - Provide the 3D similarity

  • Since first week we use clpP and Lon as our protein sequence. So, we find the protein sequence of clpP and Lon peptidase for Bulkholderia Pseudomallei in MEROPS
  1. Click Organism --> B --> Bulkholderia Pseudomallei
  2. Click SJ –S16 (SJ – clan, S16- family)
  3. Copy Lon sequence in notepad
  4. Repeat procedure 1 - 3 for SK-S14
  5. Save file
  • Searching database Protein Data Bank (pdb) using PSI-BLAST through BLAST website
  1. protein blast --> blastp
  2. Enter Query Sequence (Fasta Sequence) -->job title
  3. Choose Protein Data Bank (pdb) and Select PSI-Blast
  4. Click BLAST
  • PDB ID can be obtained from BLAST software. The PDB ID for clpP and Lon of Bulkhoderia Pseuodomallei are 1TYF4 and 1RR92. This PDB ID will be used in Protein Data Bank to download Fasta Sequence and PDB file (gz).
  1. Protein Data Bank --> Enter PDB ID --> Search
  2. Download Fasta Sequence and PDB file (gz)

F) Artemis - A genome viewer and annotation tool that allows visualisation of sequence features and results of analysis within the context of sequence and its frames translation.

  1. Artemis v5 --> File --> Open --> BPs.dbs
  2. Choose a part of sequence from notepad
  3. Go to --> navigator--> Paste the sequence in the blank to Find amino acid string --> Create
  4. Create --> Mark ORF in range --> Minimum open reading frame
  5. Delete unwanted sequence without similarity
  6. For wanted sequence: Edit -->Trim selected feature to next met
  7. Step 1 - 6 is repeated for another sequence
  8. Put the other sequence in the same entry
  9. Name the sequence: CDS --> Edit --> Edit selected feature --> Copy name from notepad --> paste in “none” --> Apply

G. RasWin Software - Provides the view of 3D structure

  1. Open file pdb file
  2. Display the structure in different types of modification and colour that represent molecule in the structure