Name: Structure and topology of RNA in living systems
Start: 2023-01-30T08:00:00+01:00
End: 2023-02-02T12:30:00+01:00
Location: ECT*

Structure and topology of RNA in living systems

from Monday, 30 January 2023 (08:00) to Thursday, 2 February 2023 (12:30)

Monday, 30 January 2023

08:30 REGISTRATION
REGISTRATION
08:30 - 09:00
Room: Entrance Rustico (brown building) ECT*
09:00 Introduction - Luca Tubiana
Introduction
- Luca Tubiana
09:00 - 09:15
Room: Aula Renzo Leonardi
Session I
Session I
09:00 - 10:30
Room: Aula Renzo Leonardi Luca Tubiana: Introduction Mauricio Comas-Garcia: Selective packaging of HIV-1 genomic RNA
09:15 Selective packaging of HIV-1 genomic RNA - Mauricio Comas-Garcia
Selective packaging of HIV-1 genomic RNA
- Mauricio Comas-Garcia
09:15 - 10:30
Room: Aula Renzo Leonardi
10:30 Coffee break
Coffee break
10:30 - 11:00
Room: Villa Tambosi

11:00 Session II
Session II
11:00 - 12:30
Room: Aula Renzo Leonardi
Using synthetic biology to unravel RNA tertiary interactions - Roee Amit
Using synthetic biology to unravel RNA tertiary interactions
- Roee Amit
11:00 - 11:45
Room: Aula Renzo Leonardi
11:45 Computational modeling of icosahedral shell assembly and encapsulation of flexible polymers - Michael Hagan
Computational modeling of icosahedral shell assembly and encapsulation of flexible polymers
- Michael Hagan
11:45 - 12:30
Room: Aula Renzo Leonardi
12:30 Lunch break
Lunch break
12:30 - 14:30
Room: Villa Tambosi

14:30 Session III
Session III
14:30 - 16:00
Room: Aula Renzo Leonardi
Spiders, entanglements, and RNA structure prediction - Marta Szachniuk
Spiders, entanglements, and RNA structure prediction
- Marta Szachniuk
14:30 - 15:15
Room: Aula Renzo Leonardi
15:15 Probing the structure and function of long viral RNAs - Redmond Smyth
Probing the structure and function of long viral RNAs
- Redmond Smyth
15:15 - 16:00
Room: Aula Renzo Leonardi
16:00 Coffee break
Coffee break
16:00 - 16:30
Room: Villa Tambosi
16:30 Molecular Dynamics to investigate Impact of RNA modifications on RNA structural dynamics and recognition - Valerio Piomponi
Molecular Dynamics to investigate Impact of RNA modifications on RNA structural dynamics and recognition
- Valerio Piomponi
16:30 - 17:00
Room: Aula Renzo Leonardi
Short talks I
Short talks I
16:30 - 17:30
Room: Aula Renzo Leonardi
17:00 WebTetrado, your assistant in the G4 space - Michal Zurkowski
WebTetrado, your assistant in the G4 space
- Michal Zurkowski
17:00 - 17:30
Room: Aula Renzo Leonardi
Tuesday, 31 January 2023
09:00 Physical models for the degradation resistance of xrRNAs - Christian Micheletti
Physical models for the degradation resistance of xrRNAs
- Christian Micheletti
09:00 - 09:45
Room: Aula Renzo Leonardi
Session IV
Session IV
09:00 - 10:30
Room: Aula Renzo Leonardi
09:45 RNA as a randomly branched polymer - Anže Božič
RNA as a randomly branched polymer
- Anže Božič
09:45 - 10:30
Room: Aula Renzo Leonardi
10:30 Coffee break
Coffee break
10:30 - 11:00
Room: Villa Tambosi
11:00 RNA secondary structures in RNA viruses - Manja Marz
RNA secondary structures in RNA viruses
- Manja Marz
11:00 - 11:45
Room: Aula Renzo Leonardi
Session V
Session V
11:00 - 12:30
Room: Aula Renzo Leonardi
11:45 Dissecting RNA dynamics combining molecular simulations and solution experiments - Giovanni Bussi
Dissecting RNA dynamics combining molecular simulations and solution experiments
- Giovanni Bussi
11:45 - 12:30
Room: Aula Renzo Leonardi
12:30 Lunch break
Lunch break
12:30 - 14:30
Room: Villa Tambosi
14:30 Conformational space exploration of minimal ribozymes for autocatalytic networks - Guillaume Stirnemann
Conformational space exploration of minimal ribozymes for autocatalytic networks
- Guillaume Stirnemann
14:30 - 15:15
Room: Aula Renzo Leonardi
Session VI
Session VI
14:30 - 16:00
Room: Aula Renzo Leonardi
15:15 Simulations of RNA structural dynamics and ligand association paths: the case of an aminoglycoside-sensing riboswitch - Joanna Trylska
Simulations of RNA structural dynamics and ligand association paths: the case of an aminoglycoside-sensing riboswitch
- Joanna Trylska
15:15 - 16:00
Room: Aula Renzo Leonardi
Wednesday, 1 February 2023
09:00 RNA structural ensembles from energy landscape explorations - Konstantin Roeder
RNA structural ensembles from energy landscape explorations
- Konstantin Roeder
09:00 - 09:45
Room: Aula Renzo Leonardi
Session VII
Session VII
09:00 - 10:30
Room: Aula Renzo Leonardi
09:45 Quantitative electrostatic force tomography for proteinaceous capsids in interaction with an approaching nanoscale substrate - Horacio V. Guzman (Universidad Autonoma de Madrid | Jozef Stefan Institute)
Quantitative electrostatic force tomography for proteinaceous capsids in interaction with an approaching nanoscale substrate
- Horacio V. Guzman (Universidad Autonoma de Madrid | Jozef Stefan Institute)
09:45 - 10:30
Room: Aula Renzo Leonardi
10:30 Coffee break
Coffee break
10:30 - 11:00
Room: Villa Tambosi
11:00 Integrative modeling strategies and RNA polymorphism - Samuela Pasquali
Integrative modeling strategies and RNA polymorphism
- Samuela Pasquali
11:00 - 11:45
Room: Aula Renzo Leonardi
Session VIII
Session VIII
11:00 - 12:30
Room: Aula Renzo Leonardi
11:45 RNA Composer-based modeling of RNA 3D structures in CASP15 - Maciej Antczak
RNA Composer-based modeling of RNA 3D structures in CASP15
- Maciej Antczak
11:45 - 12:30
Room: Aula Renzo Leonardi
12:30 Lunch break
Lunch break
12:30 - 14:30
Room: Villa Tambosi
14:30 Differential SHAPE probing to screen computationally designed RNA and to detect pseudoknot and non-canonical interactions - Bruno Sargeuil
Differential SHAPE probing to screen computationally designed RNA and to detect pseudoknot and non-canonical interactions
- Bruno Sargeuil
14:30 - 15:15
Room: Aula Renzo Leonardi
Session IX
Session IX
14:30 - 16:00
Room: Aula Renzo Leonardi

15:15 Discussion
Discussion
15:15 - 16:00
Room: Aula Renzo Leonardi

16:00 Coffee break
Coffee break
16:00 - 16:30
Room: Villa Tambosi

16:30 Discussion
Discussion
16:30 - 17:30
Room: Aula Renzo Leonardi Moderators: Samuela Pasquali, Luca Tubiana, Anže Božič
Thursday, 2 February 2023
09:00 Deciphering the mechanism of influenza A genome packaging using genome-wide approaches - Roland Marquet
Deciphering the mechanism of influenza A genome packaging using genome-wide approaches
- Roland Marquet
09:00 - 09:45
Room: Aula Renzo Leonardi
Session XI
Session XI
09:00 - 10:15
Room: Aula Renzo Leonardi
09:45 Computational 3D structure characterization of CCMV RNA2 fragment - Giovanni Mattiotti
Computational 3D structure characterization of CCMV RNA2 fragment
- Giovanni Mattiotti
09:45 - 10:15
Room: Aula Renzo Leonardi
10:15 Coffee break
Coffee break
10:15 - 10:45
Room: Villa Tambosi
10:45 Knot or not in RNA? - Wanda Niemyska
Knot or not in RNA?
- Wanda Niemyska
10:45 - 11:15
Room: Aula Renzo Leonardi
Short talks 2
Short talks 2
10:45 - 11:45
Room: Aula Renzo Leonardi
11:15 RNA Abstractions for Structural Comparison and Classification - Michela Quadrini
RNA Abstractions for Structural Comparison and Classification
- Michela Quadrini
11:15 - 11:45
Room: Aula Renzo Leonardi