Undergraduate Training Courses - Department of Pharmacy
Bioinorganic Chemistry – Molecular simulations (ECTS PDU-428): Structural Bioinformatics, Biomolecular visualization, Structure Quality assessment, Structure determination and prediction, Biomolecular simulations.  5 Practical courses.


1st Practical Course:

  • Structural Bioinformatics. Data bases (literature, genome, protein, structures, web-based applications in biomolecular applications), data searching and mining.
  • Sequence similarity search and sequence alignment. Use of ClustalW and BLAST algorithm. Applications & examples.

2nd Practical Course:

  • Protein Architecture and classification of protein structures. CATH & SCOP secondary databases. Prediction of Secondary structure elements, algorithms, web-based platforms and applications.
  • Molecular Building and Visualization.Applications and examples, use of MolMol software, analysis of various protein structure available in Protein Data Bank (PDB).

3rd Practical Course:

  • Biomolecular NMR and its application in high-resolution conformational analysis of peptides & proteins.
  • Structure comparison and analysis. Quality assessment of biomolecular structures. Applications, use of Procheck software, analysis of Xray models and NMR models ensemble available in PDB

4th Practical Course:

  • Biomolecular Simulations I: Structure prediction methodologies: Homology or Comparative modeling, Threading (Fold recognition) & ab initio structure prediction. Web-based applications, use of SwissModel (homology/comparative modeling) and Phyre (fold recognition) servers.
5th Practical Course:

Biomolecular Simulations II:     Docking simulations and principles in structure-based & computer-aided drug design. Set up of docking calculation for protein-ligand complex and analysis of ligand conformers, use of AutoDOCK Tools software.

Training course Notes. Clink here.