Computational Drug Design

Dr. Ramachandra Bhaskara
Dr. Ahmadreza Mehdipour

Presentation of the course open to all interested students

17 October 2017 14:00 s.t.
Seminarraum __.401
Fachbereich 13 Physik,
Institut für Biophysik,
Max-von-Laue-Str. 1, Goethe-Uni Frankfurt
Dr. Ramachandra Bhaskara,
Dr. Ahmadreza Mehdipour


Computational Drug Design
Structure of the course

1. Introduction to computational drug design

2. Ligand-based approaches
    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


Topic for presentation

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 Institute of Biophysics

Computational drug design
Dr. Ramachandra Bhaskara
Dr. Ahmadreza Mehdipour
Department of Theoretical Biophysics

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

Course documentation

Course announcement