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Molecular modelling and computational structural biology 2

General data

Course ID: 1000-716MM2 Erasmus code / ISCED: (unknown) / (unknown)
Course title: Molecular modelling and computational structural biology 2 Name in Polish: Modelowanie molekularne i obliczeniowa biologia strukturalna 2
Organizational unit: Faculty of Mathematics, Informatics, and Mechanics
Course groups: Elective courses for 3rd grade Bioinformatics
ECTS credit allocation (and other scores): 6.00
view allocation of credits
Language: Polish
Main fields of studies for MISMaP:

biology
biotechnology
chemistry
computer science
mathematics
physics

Prerequisites (description):

Required basic knowledge on molecular modelling methods and structural biology. Qualifications to use at least one molecular modelling environment, like NAMD/VMD, MOE or Schrodinger.

Mode:

Blended learning
Classroom

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.

Classes in period "Summer semester 2021/22" (in progress)

Time span: 2022-02-21 - 2022-06-15
Choosen plan division:


magnify
see course schedule
Type of class: Lab, 30 hours more information
Lecture, 30 hours more information
Coordinators: Bogdan Lesyng
Group instructors: Bartosz Greń, Bogdan Lesyng
Students list: (inaccessible to you)
Examination: Examination

Classes in period "Summer semester 2022/23" (future)

Time span: 2023-02-20 - 2023-06-18
Choosen plan division:


magnify
see course schedule
Type of class: Lab, 30 hours more information
Lecture, 30 hours more information
Coordinators: Bogdan Lesyng
Group instructors: Bartosz Greń, Bogdan Lesyng
Students list: (inaccessible to you)
Examination: Examination
Course descriptions are protected by copyright.
Copyright by University of Warsaw.