The objective is to introduce atomistic modeling techniques and motivate its potential for solving problems in molecular biology and biomolecular engineering, with a particular emphasis on protein investigation. Students will learn the basics of atomistic modeling, including choosing interatomic potentials, visualization and analysis of data. We will discuss limitations and potentials of atomistic modeling of biological molecules. In the second part of the class, students will work on hands-on projects in computational lab. All simulation codes and numerical tools will be explained in detail, and will be provided to participants to be used on their laptops.
Course Main Topics
Introduction to Molecular Modelling, Force fields for biomolecular modelling, Energy minimization, Molecular dynamics principles, Advanced modelling (e.g., Metadynamics), Example and applications.
1. Leach, A. R. (2001) Molecular Modelling: Principles and Applications, 2nd Edn. Pearson Prentice Hall.
2. Kukol A. (2008) Molecular Modeling of Proteins, Springer.
Pre-requirements of the Course
Basic knowledge of theoretical physics and coding
At the end of the course, a small project to be carried out with the methods described in the course will be assigned to the students. Within 2 months from the end of the course, the students, who whish to be graded and recieve the corresponding certificate, are asked to send a short report for evaluation.
Please register by using the following Registration Form. Please note that number of participants of the course is limited. Deadline for registration is April 30, 2018.
Institute of Mathematics of the National Academy of Sciences of Ukraine, Tereshchenkivska str., 3, Kyiv.
These courses are given in the framework of the Horizon 2020 project AMMODІT funded by Marie Skłodowska-Curie actions - Research and Innovation Staff Exchange (RISE-2014) H2020-MSCA-RISE-2014 Project number 645672.