Computational Drug Design
Lecturers: Dr. Kush Coshic, Dr. Balázs Fábián, Dr. Sanjoy Paul
Course open to all interested students.
Every Tuesday 14:00 – 16:00 (s.t.) during the Winter Semester
Starting date: October 15, 2024
Contact the lecturers directly:
Kush Coshic: Kush.Coshic@biophys.mpg.de
Jayashrita Debnath: Jayashrita.Debnath@biophys.mpg.de
Balázs Fábián: Balazs.Fabian@biophys.mpg.de
Sanjoy Paul: Sanjoy.Paul@biophys.mpg.de
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
- a. Molecular docking
- 5. Free energy perturbation
- 6. Enhance sampling methods
Topics for Student Presentations
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
Documentation
(password protected PDFs)
- Lecture 1: Introduction
- Lecture 2: LigandBased DD
- Lecture 3: Pharmacophore Modelling
- Lecture 4: Target Identification
- Lecture 5: Biological Sequence Analysis
- Lecture 6: Homology Modeling
- Lecture 7: Ligand Docking
- Lecture 8: PPI Docking
- Lecture 9: Intro to MD
- Lecture 10: Ligand Binding Affinity
- Lecture 11: Alchemical Free Energy Calculations
- Lecture 12: Enhanced Sampling
- Lecture 13: AI4CADD1
- Lecture 14: AI4CADD2
- Lecture 15: Drug Design in the Pharmaceutical Industry (Guest Lecture)
