Introduction to bioinormatics and modelling 1100-5PM15
Topics covered in the course of the lecture:
A) molecular mechanics
- force fields
- full-atom and coarse-grained models
- potential energy in force fields
B) conformational space sampling methods
- Monte Carlo
- molecular dynamics
- enhanced sampling methods
C) modeling of the biological environment
- simplified models of solvation
- crowding effects in biological systems
D) selected aspects of molecular simulation analysis
- analysis of structure, dynamics and thermodynamics of systems
- computer simulations against experimental data
E) bioinformatics issues
- comparison of protein sequences
- prediction of protein structures
F) computer-aided drug design
- molecular databases
- prediction of ligand-receptor interactions
- QSAR models
Exercises using computers will be devoted to practical applications of selected methods presented during lectures.
Student workload:
- lecture - 30 hours
- exercises - 30 hours
- preparation for classes and solving homework assignments - 30 hours
- preparing for the exam - 30 hours
a total of 120 hours
Main fields of studies for MISMaP
physics
biotechnology
Mode
Prerequisites (description)
Course coordinators
Learning outcomes
(KNOWLEDGE) as a result of participation in classes, the student:
- has basic knowledge of molecular modeling: molecular mechanics and dynamics, Monte Carlo methods (K_W02)
- knows basic concepts of bioinformatics and computer-aided drug modeling (K_W03, K_W07)
(SKILLS) as a result of participation in classes, the student:
- is able to select a computational method for the scientific problem set before him (K_U02)
- is able (to a basic extent) to use selected molecular modeling tools and selected bioinformatics tools (K_U03)
- is able to use selected molecular databases (K_U04)
(SOCIAL COMPETENCES) as a result of participation in the class, the student:
- understands the importance of complementarity of experimental and computational techniques of modern biophysics (K_K03)
Assessment criteria
Permissible number of absences to pass the course: 2 for the lecture and 2 for the exercises. In exceptional cases, instructors may allow to make up for absences at the exercises on the basis of a report from an independently done exercise, and lectures - on the basis of an oral colloquium.
Final exam in written form.
Bibliography
1. Andrew Leach, Molecular Modelling: Principles and Applications
2. Daan Frenkel, Berend Smit, Understanding molecular simulation
3. Arthur Lesk, Introduction to Bioinformatics
4. Mike Williamson, How proteins work
5. The current literature references provided at the lectures.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: