Advances in Molecular Modeling Workshop
from
Monday 9 December 2024 (01:45)
to
Tuesday 10 December 2024 (16:20)
Monday 9 December 2024
08:30
Registration
Registration
08:30 - 09:00
Room: Auditorium A
09:00
Introduction
Introduction
09:00 - 09:15
Room: Auditorium A
09:15
Uncovering antibody sequences and structures, their assembly and their conformational flexibility
-
Franca Fraternali
(
University College London London, England
)
Uncovering antibody sequences and structures, their assembly and their conformational flexibility
Franca Fraternali
(
University College London London, England
)
09:15 - 10:00
Room: Auditorium A
10:00
Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques
-
Eva Smorodina
(
University of Oslo
)
Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques
Eva Smorodina
(
University of Oslo
)
10:00 - 10:15
Room: Auditorium A
10:15
Coffee break
Coffee break
10:15 - 10:45
Room: Auditorium A
10:45
Workshop: Combining experiments and simulations: theory and practical examples for disordered proteins
-
Kresten Lindorff-Larsen
(
Department of Biology, University of Copenhagen, Copenhagen, Denmark
)
Workshop: Combining experiments and simulations: theory and practical examples for disordered proteins
Kresten Lindorff-Larsen
(
Department of Biology, University of Copenhagen, Copenhagen, Denmark
)
10:45 - 12:00
Room: Auditorium A
12:00
Lunch Break
Lunch Break
12:00 - 13:00
Room: Auditorium A
13:00
Simulating entire cells with Martini
-
Siewert Jan Marrink
(
Faculty of Science and Engineering Engineering, University of Groningen Groningen, The Netherlands.
)
Simulating entire cells with Martini
Siewert Jan Marrink
(
Faculty of Science and Engineering Engineering, University of Groningen Groningen, The Netherlands.
)
13:00 - 13:45
Room: Auditorium A
13:45
Workshop: Mastering Parametrization in Martini 3: Tips and Tricks for Small Molecules and Lipids
-
Paulo Cesar Telles de Souza
(
ENS de Lyon, CNRS CNRS, Franc
)
Workshop: Mastering Parametrization in Martini 3: Tips and Tricks for Small Molecules and Lipids
Paulo Cesar Telles de Souza
(
ENS de Lyon, CNRS CNRS, Franc
)
13:45 - 15:15
Room: Auditorium A
https://github.com/Martini-Force-Field-Initiative/CopenhagenWorkshop2024
15:15
Coffee Break
Coffee Break
15:15 - 15:45
Room: Auditorium A
15:45
An integrative MD model reveals protein complexes and protein distribution in mitochondria
-
Fabian Schuhmann
(
Niels Bohr Institute, University of Copenhagen
)
An integrative MD model reveals protein complexes and protein distribution in mitochondria
Fabian Schuhmann
(
Niels Bohr Institute, University of Copenhagen
)
15:45 - 16:00
Room: Auditorium A
16:00
Investigating the role of cholesterol in regulating the SLC7 family of amino acid transporters
-
Dimitrios Kolokouris
(
University of Copenhagen
)
Investigating the role of cholesterol in regulating the SLC7 family of amino acid transporters
Dimitrios Kolokouris
(
University of Copenhagen
)
16:00 - 16:15
Room: Auditorium A
16:15
PINning down the elevator-type mechanism of auxin transport
-
Lorena Zuzic
(
Aarhus University
)
PINning down the elevator-type mechanism of auxin transport
Lorena Zuzic
(
Aarhus University
)
16:15 - 16:30
Room: Auditorium A
16:30
Advanced Sampling Methodology for Investigating Early-Stage Amyloid Aggregation Structures
-
Ali Asghar Hakami Zanjani
(
University of Southern Denmark
)
Advanced Sampling Methodology for Investigating Early-Stage Amyloid Aggregation Structures
Ali Asghar Hakami Zanjani
(
University of Southern Denmark
)
16:30 - 16:45
Room: Auditorium A
16:45
Pore formation in complex biological membranes
-
Leonhard Starke
(
Aarhus University
)
Pore formation in complex biological membranes
Leonhard Starke
(
Aarhus University
)
16:45 - 17:00
Room: Auditorium A
17:00
Poster Session
Poster Session
17:00 - 18:00
Room: Auditorium A
18:00
Social Dinner
Social Dinner
18:00 - 21:00
Room: Auditorium A
Tuesday 10 December 2024
09:00
Navigating protein landscapes with a machine learned transferable coarse-grained model
-
Cecilia Clementi
(
Free University of Berlin Berlin, Germany
)
Navigating protein landscapes with a machine learned transferable coarse-grained model
Cecilia Clementi
(
Free University of Berlin Berlin, Germany
)
09:00 - 09:45
Room: Auditorium A
09:45
Role of the sequnce length in the coil-to-globule transition of elastin-like polypeptides
-
Tatiana Morozova
(
CNRS/Institut Pasteur
)
Role of the sequnce length in the coil-to-globule transition of elastin-like polypeptides
Tatiana Morozova
(
CNRS/Institut Pasteur
)
09:45 - 10:00
Room: Auditorium A
10:00
Group picture of attendees in front of NBI
Group picture of attendees in front of NBI
10:00 - 10:15
Room: Auditorium A
10:15
Coffee Break
Coffee Break
10:15 - 10:45
Room: Auditorium A
10:45
Workshop: Enhanced Sampling Simulation Methods for Thermodynamics, Kinetics, and Pathways
-
Edina Rosta
(
University College London London, England
)
Workshop: Enhanced Sampling Simulation Methods for Thermodynamics, Kinetics, and Pathways
Edina Rosta
(
University College London London, England
)
10:45 - 12:00
Room: Auditorium A
https://github.com/rostaresearch/enhanced-sampling-workshop-2022/
12:00
Lunch Break
Lunch Break
12:00 - 13:00
Room: Auditorium A
13:00
Simulations of active vesicles
-
Dmitry Fedosov
(
Forschungszentrum Jülich GmbH Wilhelm Johnen StraßeStraße, Jülich Germany
)
Simulations of active vesicles
Dmitry Fedosov
(
Forschungszentrum Jülich GmbH Wilhelm Johnen StraßeStraße, Jülich Germany
)
13:00 - 13:45
Room: Auditorium A
13:45
On the sampling of simulations of membrane shape
-
Adria Bravo Vidal
(
Niels Bohr Institute, University of Copenhagen
)
On the sampling of simulations of membrane shape
Adria Bravo Vidal
(
Niels Bohr Institute, University of Copenhagen
)
13:45 - 14:00
Room: Auditorium A
14:00
Workshop: Mesoscale simulation of biomembranes with FreeDTS
-
Weria Pezeshkian
(
Niels Bohr Institute, University of Copenhagen, Denmark
)
Workshop: Mesoscale simulation of biomembranes with FreeDTS
Weria Pezeshkian
(
Niels Bohr Institute, University of Copenhagen, Denmark
)
14:00 - 15:00
Room: Auditorium A
https://github.com/weria-pezeshkian/FreeDTS/wiki/Workshop-2024
15:00
Coffee break and GoodBye
Coffee break and GoodBye
15:00 - 16:00
Room: Auditorium A