Molecular modelling and computational structural biology 1 1100-3BP14

Educational Content:
From protein sequence and structure to protein dynamics and function. Overview of basic methods for protein sequence and structure analysis. Prediction of protein structure by homology modeling methods and use of AlphaFold2. Fundamentals of molecular mechanics and dynamics methods and their applications in structure and dynamics studies with popular molecular modeling packages. Physics of protein interactions with low molecular weight ligands. Use of a selected popular modeling package in docking processes. The lab will utilize publicly available NAMD/VMD and AutoDock packages and commercial MOE and/or Schrodinger, Molecular Conceptor software packages, to name a few.

The lab covers the following classes:
Introduction: Overview of the basic functions of selected molecular modeling packages.
Exercise #1: Analysis of protein structure (protein ordering).
Exercise #2: Selected dimer stability analysis (selection of proteins, system preparation, system molecular mechanics and dynamics simulations, result analysis).
Exercise #3: Analysis of the effect of selected NSAIDs on COX-1 and COX-2 proteins (system preparation, docking, result analysis).

Type of course

obligatory courses

Prerequisites (description)

(in Polish) Zakres wiedzy z Pracowni Technologii Informacyjnej z I roku uznawany przez prowadzącego za podstawowy: znajomość edytora vi lub vim, podstawowe polecenia powłokowe (1.metaznaki (*,? i [...] oraz rozwijające nazwy ścieżek); 2.wyrażenia regularne (znak kropki, symbole: $, ^,*,[] i [^], {m,n}, (...), operatory rozszerzające w egrep i awk); 3.filtry (polecenia: grep, egrep, fgrep, cut, sort, uniq, tr, edytor strumieniowy sed, filtr tekstowy awk); 4.przeadresowania wejścia-wyjścia (operator: >, <, >>, <<[-]ogr, 2>, 2>&1, zmienna noclobber), 4.potoki (polecenie tee))oraz ssh i scp- materiały dostępne na www.bioexploratorium.pl/wiki Zakres wiedzy ze znajomości struktury i właściwości podstawowych aminokwasów - polecana książka: Biochemia L. Stryer.

Course coordinators

Krystiana Krzyśko

Learning outcomes

Students learn the basics of mathematical modeling and computer biomolecular systems, dynamics and simulation of selected regulatory processes using the methods of mechanic and molecular
dynamics, Monte-Carlo methods, molecular models, and the basics of systems theory. Students become familiar with well-known and popular molecular modeling and design packages as well as
the virtual reality technology. The lecture and exercises prepare students for independent modeling of biomolecular systems and designing of enzyme inhibitors – potential drugs.

Bibliography

Tutorial for MOE (https://www.chemcomp.com/moe/help/latest/index_tut.html)
Tutorial for VMD i NAMD (http://www.ks.uiuc.edu/Training/Tutorials/)
Tutorial for Yasara
Lecture materials (available on the Kampus2 platform)
Molecular Conceptor lectures - available on lab computers

Additional information

Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:

Applications of Physics in Biology and Medicine, first cycle programme

Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system:

Description of 1100-3BP14 in USOSweb