Computational Drug Design

Computational Drug Design

Lecturers: Dr. Ramachandra M. Bhaskara, Dr. Jayashrita Debnath, Dr. Balázs Fábián, Dr. Tobias Hüfner

Course open to all interested students.
Every Tuesday 14:00 – 16:00 (s.t.) during the Winter Semester

Contact the lecturers directly:
Ramachandra M. Bhaskara:
Jayashrita Debnath:
Balázs Fábián:
Tobias Hüfner:

Content Covered (incl. practicals)

  • 1. Introduction to computational drug design
  • 2. Ligand-based approachees
    • a. (Quantitative) structure-activity relationship (SAR & QSAR)
    • b. Pharmacophore modeling
  • 3. Bioinformatics approaches (target recognition and structural modeling)
    • a. Sequence alignments and searches
    • b. Gene identification and prediction
    • c. Homology modeling
  • 4. Structure-based approaches
    • a. Molecular docking
      • i. Ligand docking: theory and scoring functions
      • ii. Virtual screening
      • iii. Protein-protein docking and interaction
    • b. Molecular dynamics simulation
      • i. Introduction into molecular dynamics
      • ii. Estimation of ligand binding affinity
  • 5. Free energy perturbation
  • 6. Enhance sampling methods

Topics for Student Presentations


  • 1. QSAR modeling using partial least square (PLS)
  • 2. Application of neural networks in QSAR


  • 1. Profile based methods and applications to sequence alignment
  • 2. Threading for protein structure prediction
  • 3. Using co-evolution for protein structure prediction


  • 1. Protein-protein interface prediction using 3D structure and residue conservation
  • 2. Induced-fit docking

MD simulation

  • 1. Thermodynamic integration (TI) for free energy calculation
  • 2. Non-equilibrium simulation
  • 3. Advanced methods in enhanced sampling
  • 4. Metadynamics


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