Methods in Protein Modeling
Course description:
Detailed understanding of protein structure and function is a prerequisite for
unravelling biological
systems and molecular networks, and for development of new drugs for treatment of
diseases. The
course aims to enable the student to understand protein structure and related
computational
techniques to investigate protein structure. This is important regarding protein
function in
biological systems, understanding protein interactions, design of protein-targeting
drugs and
protein-based drugs, and optimization of enzyme activities.
Recommended Books:
1. Na´ray-Szabo´, G. (Ed.). (2014). Protein modelling. Springer International
Publishing.
2. Kukol, A. (Ed.). (2008). Molecular modeling of proteins (Vol. 443). Totowa, NJ::
Humana
Press.
3. Maia, R. T., de Moraes Filho, R. M., and Campos, M. D. A. (Eds.). (2021).
Homology
Molecular Modeling: Perspectives and Applications. BoD–Books on Demand.
Course Learning Outcomes:
After completing this course, students will understand the various levels of protein
structure and
their graphical representation. They will predict and interpret the structural
information and the
structure-function relationships of biological macromolecules.
Assessment system:
Quizzes 10-15%
Assignments 5-10%
MSE 30-40%
ESE 40-50%
Lecture Plan:
S.NO. Lecture Topic Quizzes Assignments
1.Fundamentals of protein biochemistry and protein structure
2. Protein structure databases
4. Data visualization methods
5. Bioanalytical techniques for protein structure analysis
6. Methods of protein Modeling
7. Protein interactions
8. Fundamentals of protein biochemistry and protein structure
9. Aspects of High-performance computing
10. Molecular mechanics methods for protein modelling
11. Analysis of molecular mechanics trajectories. Constraint
based protein modelling
12.Docking
13.Homology modelling