Molecular modelling and computational structural biology 2

General data

Course ID:	1100-3BP23
Erasmus code / ISCED:	11.953 Kod klasyfikacyjny przedmiotu składa się z trzech do pięciu cyfr, przy czym trzy pierwsze oznaczają klasyfikację dziedziny wg. Listy kodów dziedzin obowiązującej w programie Socrates/Erasmus, czwarta (dotąd na ogół 0) – ewentualne uszczegółowienie informacji o dyscyplinie, piąta – stopień zaawansowania przedmiotu ustalony na podstawie roku studiów, dla którego przedmiot jest przeznaczony. / (0619) Information and Communication Technologies (ICTs), not elsewhere classified The ISCED (International Standard Classification of Education) code has been designed by UNESCO.
Course title:	Molecular modelling and computational structural biology 2
Name in Polish:	Modelowanie molekularne i obliczeniowa biologia strukturalna cz. II
Organizational unit:	Faculty of Physics
Course groups:
ECTS credit allocation (and other scores):	(not available) Basic information on ECTS credits allocation principles: the annual hourly workload of the student’s work required to achieve the expected learning outcomes for a given stage is 1500-1800h, corresponding to 60 ECTS; the student’s weekly hourly workload is 45 h; 1 ECTS point corresponds to 25-30 hours of student work needed to achieve the assumed learning outcomes; weekly student workload necessary to achieve the assumed learning outcomes allows to obtain 1.5 ECTS; work required to pass the course, which has been assigned 3 ECTS, constitutes 10% of the semester student load. view allocation of credits
Language:	Polish
Main fields of studies for MISMaP:	biology biotechnology chemistry computer science mathematics physics
Prerequisites (description):	(in Polish) Wymagana podstawowa wiedza dotycząca metod molekularnego modelowania i obliczeniowej biologii strukturalnej. Umiejętność pracy w przynajmniej jednym środowisku modelowania układów (bio)molekularnych, takich jak NAMD/VMD, MOE lub Schrodinger.
Short description:	From Born-Oppenheimer approximation to a mechanical model of (bio)molecular systems. Determination of stable structual states - local and global energy minimization methods. Molecular motions - microscopic molecular dynamics and mezoscopic Brownian Dynamics. Monte-Carlo methods and free-energy simulations. Physics and molecular evolution processes. Molecular folding mechanisms. Biomolecular recognition processes. Complex systems and biomolecular machines. Biomolecular machines and complex systems.
Full description:	From Born-Oppenheimer approximation to a mechanical model of (bio)molecular systems. Microscopic and mezoscopic interaction potentials. Hydrodynamic interactions. Determination of stable structual states - local and global energy minimization methods. Steepest descend and Newton-Raphson methods, operators allowing smoothing the energy hypersurface. Examples of stable strucures of nucleic acids and proteins. A, B and Z DNA. Protein folds. Structure comparison methods for proteins and nucleic acids. Homology of sequences and structures. Molecular motions - microscopic classical and quantum molecular dynamics, and mezoscopic Brownian Dynamics. Description of algoritms and stability analysis. Monte-Carlo methods and free-energy simulations. Thermodynamic perturbational approach. Computational alchemy. Physics and molecular evolution processes. Molecular folding mechanisms. Biomolecular recognition processes. Complex systems and biomolecular machines. Biomolecular machines and complex systems. From rate constants to signaling and regulation systems. Examples of oncogenic mutations and their influence on regulation processes.
Bibliography:	1. D.W.Heermann, Podstawy symulacji komputerowych w fizyce, WNT, Warszawa, 1997. 2. Robert Kosiński, Wprowadzenie do mechaniki kwantowej i fizyki statystycznej, Oficyna Wydawnicza Politechniki Warszawskiej, Warszawa 2006. 3. L.Piela, Ideas of Quantum Chemistry, PWN, Warsaw, or another textbook in molecular quantum mechanics 4. P.O.J. Dcherer, S.F. Fischer, Theoretical Molecular Biophysics, Springer, Heidelberg, 2010 (ISBN 978-3-540-85609-2) 5. A.R.Leach, Molecular Modelling: Principles and Applications (2nd Edition), Prentice Hall; ISBN: 0582382106, 2001. 6. Materials to lectures http://kms.bioexploratorium.pl/
Learning outcomes:	Teaching students mathematical and computational moledcular modeling methods, simulations of selected processes using molecular mechanics and dynamics methods, Monte-Carlo methods, and basics of systems theory. Lecture and excercises allow students modeling biomolecular systems and design of enzyme ihibitors - potential drugs.
Assessment methods and assessment criteria:	Credits for two exercises and the exam in a form of a test.
Practical placement:	Possible practices in the Institute of Experimental and Clinical Medicine PAS in Warsaw.

This course is not currently offered.

Course descriptions are protected by copyright.
Copyright by University of Warsaw.