Monday, October 21, 2024
16:30 - 18:30
Registration
16:30 - 18:30
Opening Mixer
Tuesday, October 22, 2024
8:00 - 18:00
Registration
8:30 - 8:40
Welcome and Opening Remarks
Giulia Palermo, University of California, Riverside, USA, Chair
Session I: Structure and Dynamics
Giulia Palermo, University of California, Riverside, USA, Chair
8:40 - 9:15
Manidipa Banerjee, Indian Institute of Technology, Delhi, India
Structural Dynamics of a Non-Enveloped Virus During Disassembly
9:15 – 9:50
Yuji Sugita, RIKEN Center for Biosystems Dynamic Research, Japan
Integrative Modeling of Protein Structure and Dynamics Using MD Simulations and Experimental Data
9:50 - 10:25
Hong Zhou, University of California, Los Angeles, USA
AI-Based Methods to Overcome the Preferred Orientation and Missing-Wedge Problems in Cryo-EM and Cryo-ET
10:25 - 10:55
Coffee Break
Session II: Methodological Advances in Cryo-EM
Alessandra Magistrato, International School for Advanced Studies, Italy, Chair
10:55 - 11:30
Paulina Dominiak, University of Warsaw, Poland
Exploiting the Full Potential of Cryogenic Electron Microscopy Maps
11:30 - 12:05
Jose-Maria Carazo, Spanish National Center for Biotechnology, Spain
Zernike3d and Hetsiren for Conformational and Compositional Heterogeneity Analysis of Cryo-EM Images
12:05 - 14:00
Lunch
Session III: Cryo-EM Applications
Joanna Trylska, University of Warsaw, Poland, Chair
14:00 – 14:35
Abhishek Singharoy, Arizona State University, USA
Ice-Cream: Integrated Cyberinfrastructure for Ensemble Cryo-EM Applications & Modeling
14:35 - 15:10
Audrone Lapinaite, Arizona State University, USA
Understanding the Molecular Mechanism of Genome Editors to Enhance their Precision and Targeting Scope
15:10 – 15:30
Ivaylo Ivanov, Georgia State University, USA *
Molecular Architecture and Functional Dynamics of the Pre-Incision Complex in the Nucleotide Excision DNA Repair Pathway
15:30 – 15:50
Matthew Holcomb, Scripps Research Institute, USA *
CRYOXKIT: Incorporation of Experimental Structural Density into Autodock for Improved Pose Prediction
15:50 – 16:10
Milosz Wieczór, Gdańsk University of Technology, Poland *
Inferring the Conformational Landscape of Multistate Protein Assemblies Using Coarse-Grained Sampling of Transition Pathways
16:20 - 18:20
Poster Session I
18:20
Dinner on Own
Wednesday, October 23, 2024
8:00 - 18:00
Registration
Session IV: Structure and Dynamics
Rommie Amaro, University of California, San Diego, USA, Chair
8:30 - 9:05
Janusz Bujnicki, International Institute of Molecular and Cell Biology, Poland
Computational Modeling of RNA 3D Structures and Interactions - With and Without the Use of Experimental Data
9:05 – 9:40
Pilar Cossio, Flatiron Institute, USA
Probability Distributions from Individual Cryo-EM Images and Molecular Dynamics
9:40 - 10:15
Massimilliano Bonomi, Pasteur Institute, France
Protein Structural Ensembles from 3D and 2D Cryo-EM Data
10:15 - 10:45
Coffee Break
Session V: Cryo-EM Applications
Gabriel Lander, Scripps Research Institute, USA, Chair
10:45 - 11:20
Elizabeth Kellogg, St. Jude Children’s Research Hospital, USA
New Frontiers in Understanding and Improving RNA-Guided DNA Integration Using Cryo-EM and Machine Learning
11:20 – 11:55
Sebastian Glatt, Jagiellonian University Krakow, Poland
Translational Control of Eukaryotic Gene Expression
11:55 - 12:15
Mingxu Hu, Tsinghua University, China *
CRYOPROS: Addressing Preferred Orientation in Single-Particle Cryo-EM Through AI-Generated Auxiliary Particles
12:15 - 14:10
Lunch
Session VI: Methodological Advances in Cryo-EM
Giulia Palermo, University of California, Riverside, USA, Chair
14:10 – 14:45
Paul Emsley, MRC Laboratory of Molecular Biology, United Kingdom
Model-Building, Refinement and Validation With COOT
14:45 - 15:20
Sergio Cruz León, Max Planck Institute of Biophysics, Germany
Enabling Visual Proteomics by High-Confidence 3D Template Matchings
15:20 – 15:40
Elisa Posani, International School for Advanced Studies, Italy *
All Atom Molecular Dynamics Simulations Enable Ensemble Refinement of Flexible and Mismodelled Cryo-EM Derived RNA Structures
15:40 – 16:00
Colin Kinz-Thompson, Rutgers University-Newark, USA *
Measuring the Biomolecular Information Content Present in Structural Data
16:00 – 16:20
Lorenzo Casalino, University of California, San Diego, USA *
Harnessing Molecular Simulations to Design Stabilized Sars-Cov-2 S2 Antigens
16:20 - 18:20
Poster Session II
20:00 - 22:00
Banquet Dinner at the Savoia Excelsior Hotel
Thursday, October 24, 2024
8:00 - 15:00
Registration
Session VII: Structure and Dynamics
Joanna Trylska, University of Warsaw, Poland, Chair
8:30 - 9:05
Natalie Strynadka, University of British Columbia, Canada
Structure-Guided Drug Discovery Targeting Antibiotic Resistance Mechanisms in Staphlococcus Aureus
9:05 - 9:40
Florence Tama, RIKEN Center for Computational Science, Japan
Exploring Continuous Conformational Variability Via Cryo-EM Single-Particle Imaging and MD Simulations
9:40 - 10:15
David Taylor, University of Texas at Austin, USA
Reengineering CRISPR-Cas Effector Complexes
10:15 – 10:45 AM
Coffee Break
Session VIII: Cryo-EM Applications
Gabriel Lander, Scripps Research Institute, USA, Chair
10:45 - 11:20
Wojciech Galej, European Molecular Biology Laboratory, France
Structural Studies of the Pre-mRNA Splicing Machinery
11:20 – 11:40
Vivek Sharma, University of Helsinki, Finland *
Molecular Insights into Mitochondrial Energy Production by Integrating Cryo-Electron Microscopy and Biochemistry with Computer Simulations
11:40 – 12:00
Erik Thiede, Flatiron Institute, USA *
Towards Quantitative Recovery of Probability Densities from Cryo-EM
12:00 - 14:00
Lunch
Session IX: Methodological Advances in Cryo-EM
Joanna Trylska, University of Warsaw, Poland, Chair
14:00 - 14:35
James Fraser, University of California, San Francisco, USA
Uncovering Protein Ensembles: Automated Multiconformer Model Building for Cryo-EM Proteins, Nucleic Acids, Solvent, and Ligands
14:35 – 15:10
Mateusz Sikora, Malopolska Center of Biotechnology, Poland
Title to be Announced
15:10
Free Time & Dinner on Own
Friday, October 25, 2024
8:00 - 12:00
Registration
Session X: Structure and Dynamics
Lorenzo Casalino, University of California, San Diego, USA, Chair
8:30 - 9:05
Michele Vendruscolo, University of Cambridge, United Kingdom
Determination of Protein Structural Ensembles Using Cryo-Electron Microscopy
9:05 – 9:40
Erik Lindahl, Stockholm University, Sweden
Modeling Conformational Transition of Proteins by Combining Cryo-EM, Alphafold and Molecular Simulations
9:40 - 10:15
Isabelle Rouiller, University of Melbourne, Australia
Characterizing the Conformational Landscape of the Hexameric VCP Complex from 2D Cryo-EM Images Using Molecular Dynamics Simulation
10:15 - 10:45
Coffee Break
Session XI: Cryo-EM Applications
Alessandra Magistrato, International School for Advanced Studies, Italy, Chair
10:45 - 11:05
Jakub Rzeszótko, Max Planck Institute of Molecular and Cell Biology and Genetics, Germany *
Advancing Structural Insights into Small Membrane Transporters Through SP-Cryo-EM: Unraveling the Regulatory Mechanisms of SLC26 Family
11:05 - 11:25
Nathan Bernhardt, National Institutes of Health, USA *
What Determines the Dwell-Time of a Bound Lipid? Interpreting Lipid Densities in Structural Data Using Molecular Dynamics Simulations and Specialized Tools for Their Analysis
11:25 - 11:45
Tatiana Shugaeva, KTH Royal Institute of Technology, Sweden *
Accurate Protein Fitting into Cryo-EM Maps Using Multiple Conformers Generated by Alphafold2
11:45 - 12:00
Closing Remarks and Biophysical Journal Poster Awards
Giulia Palermo, University of California, Riverside, USA
* Short Talks selected from among submitted abstracts