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
Dozenten:
Dr. Ramachandra Bhaskara,
Dr. Ahmadreza Mehdipour

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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

QSAR
1. QSAR modeling using partial least square (PLS)
2. Application of neural networks in QSAR
 
Modeling
1. Profile based methods and applications to sequence alignment
2. Threading for protein structure prediction
3. Using co-evolution for protein structure prediction
 
Docking
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