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Giancarlo Franzese <[log in para visualizar]>
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Fri, 3 Jun 2022 18:22:25 +0200
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De posible interés para los miembros de la lista.

Giancarlo Franzese


Dear colleagues and friends,
The advanced course Macromolecule MD simulations for Interdisciplinary
Beginners is aimed at novice practitioners of molecular simulations at
the graduate or early postdoctoral level. Molecular dynamics (MD)
simulations of macromolecules and their interactions with drugs and
other small-molecule ligands have advanced greatly in the recent past.
Many current examples illustrate that computational approaches can
suggest testable molecular hypotheses to explain experimentally observed
behaviours and shed light on molecular processes. Simulations of even
very large systems are now within reach, and standardization has made it
possible for novice users to learn how to apply MD methods to any
suitable system.

The course consists of theoretical lectures that will introduce
different computational methods and approaches used to study a wide
range of biomolecular systems and give students a theoretical foundation
in each method.  Then each method will be introduced during practical
sessions in a PC classroom when participants will learn the practical
steps of the work with different programs (like Gromacs, Amber, VMD,
Schrodinger package, etc.) and they will be able to try various
computational methods on the actual biomolecular systems. The
participants will also have the opportunity to apply the computational
methods to the biomolecular system of their interest.

Particular focus will be given to the study of the interaction between
bio-macromolecules and ligands, molecular docking and parametrization of
various different ligands for the empirical force fields used in MD
simulations. Additionally, we will teach how to set up the simulation of
membrane proteins, and students will also learn the basics of
coarse-grained simulations.

The advanced course will be held at the Academic and University Center
at Nove Hrady, Czech Republic, which has a rich history of organizing
FEBS practical courses, namely the course "Advanced Methods in
Macromolecular Crystallization" organized since 2004 every second year
and "Ligand-binding theory and practice" in 2014, 2016, 2018.

Nove Hrady is located in the south of the Czech Republic. The Academic
and University Center resides in a very stylish chateau, which provides
many facilities such as two lecture halls, laboratories, apartments, and
a student dormitory.

Babak Minofar, David van der Spoel, Sarah Harris, Victor Guallar
Course Organizers

                  Dr. Babak Minofar

Laboratory of Structural Biology and Bioinformatics,
Institute of Microbiology of the Czech Academy of Sciences,
Faculty of Science, University of South Bohemia,
České Budějovice, Czech Republic


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