Computational Drug Design

Dr. Ramachandra Bhaskara
Dr. Ahmadreza Mehdipour

Presentation of the course open to all interested students

16 October 2018, 14:00 s.t.

Seminarraum __.401
Fachbereich 13 Physik,
Institut für Biophysik,
Max-von-Laue-Str. 1, Goethe-Uni Frankfurt
Computational Drug Design (Course structure)
The lectures are scheduled for 2 hours per week, the exercises for 3 hours per week (including 0.5 hr theory) in a two-week intervals (2.5V + 1.5Ü = 4 SWS); the dates for the exercises will be announced later.

Further information will be posted at the Institute of Biophysics.
If you have any questions, please contact the lecturers:
Dr. Ramachandra Bhaskara ramachandra.bhaskara(at)
Dr. Ahmedreza Mehdipour ahmadreza.mehdipour(at)
the secretariat of the Institute of Biophysics,
Mrs Christine Storck-Ratnam (069/798-46410)

Content covered in lectures (including 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
       1. Free energy perturbation
       2. 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


Max-Planck-Institut für Biophysik

Computational drug design
Dr. Ramachandra Bhaskara
Dr. Ahmadreza Mehdipour
Abteilung Theoretische Biophysik

Tel.: +49 (0) 69 6303-2513
E-Mail: ramachandra.bhaskara(at)
E-Mail: ahmadreza.mehdipour(at)

Course documentation

Course announcement