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Sunday, 19 May 2024
Academy of Athens, Central Building, East Conference Room
16:00-18:00 Registration
18:00 Welcome Remarks: 
Zoe Cournia
(ISQBP President),
Lucas Papademos (President of the Board, Biomedical Research Foundation, Academy of Athens, Greece)
18:15-18:20 Introduction to the Computational Biology Award Laurate
18:20-19:20 Computational Biology Award Lecture
Johan Åqvist, Uppsala University, Sweden, “Computer Simulations of the Temperature Dependence of Enzyme Reactions”
19:30-22:00 Welcome Reception
Monday, 20 May 2024
Academy of Athens, Central Building, East Conference Room
09:00-12:40 Free Energy

Chair: Marco de Vivo

09:00-09:30 William Jorgensen, Yale University, USA, “Evolution of Computer-Aided Drug Discovery”
09:30-10:00 Charlie Brooks, University of Michigan, USA, “High-throughput approaches to free energy calculations in ligand discovery and protein design”
10:00-10:30 Alex Mackerell, University of Maryland, USA,“Site Identification by Ligand Competitive Saturation (SILCS) as a Platform Technology for Computational Investigations of Free Energies of Intermolecular Interactions”
10:30-11:15 Coffee Break
11:15-11:35 Jonas Kaidl, Schrodinger, Germany, “Is The Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?”
11:35-12:05 Klaus Liedl, University of Innsbruck, Austria, Quantifying Thermodynamic Properties in Biological Systems by Grid Inhomogeneous Solvation Theory”
12:05-12:25 Nour Aldin Kahlous, Uppsala University, Sweden, “Design of drug efficacy guided by free energy simulations of G protein-coupled receptors”
12:25-12:40 Nishita Mandal, Adam Mickiewicz University, Poland, “Beyond the Threshold: Delving into Rare Gate Opening Events in Enzyme Tunnels through Enhanced Molecular Dynamics Simulations”
12:40-14:00 Free time-Lunch on your own
14:00-18:20 Biomolecular Dynamics I

Chair: Roland Stote

14:00-14:30 Carol Post, Purdue University, USA, “Syk tyrosine kinase association with immunoreceptors: MD simulation unravels the physical basis for a new phospho-sensor regulating this protein-protein interaction”
14:30-15:00 Ellinor Haglund, University of Hawaii Manoa, USA, “Exploring Pierced Lasso Topologies: Novel Insights into Protein Folding, Function, and Therapeutic Potential”
15:00-15:20 Jan Brezovsky, Adam Mickiewicz University, Poland, “Exposing unseen passages for ligand transport through proteins and their functional consequences”
15:20-15:50 Frauke Gräter, Heidelberg Institute for Theoretical Studies, Germany, “Learning force fields and reactivity to enhance classical biomolecular simulations”
15:50-16:30 Coffee Break
16:30-17:00 Wonpil Im, Lehigh University, USA, “What can CHARMM-GUI do for you?”
17:00-17:20 Jennifer Sapia, University of Fribourg, Switzerland, “Computational insights into the mechanism of triglycerides formation: a study of DGAT1 using molecular dynamics”
17:20-17:40 Paulo Siani, Università degli Studi di Milano Bicocca, Italy, “Mechanistic Insights from Molecular Dynamics Simulations in Nanomedicine Research”
17:40-18:00 Thibault Tubiana, CNRS, France, “Molecular modelling, homo-oligomerisation and membrane interactions of hepatitis E virus pORF1 replication polyprotein”
18:00-18:20 Fabrizio Pucci, Université Libre de Bruxelles, Belgium, “Leveraging structural and (co)evolutionary data for protein fitness prediction
Tuesday 21 May 2024
Academy of Athens, Central Building, East Conference Room
09:00-12:30 Quantum Mechanics and Quantum Computing

Chair: Julian Tirado-Rives

09:00-09:30 Jean-Philip Piquemal, University of Sorbonne, France, “Hybrid Quantum-classical algorithms for Accurate Quantum Chemistry”
09:30-10:00 Nancy Makri, University of Illinois, Urbana-Champaign, USA, “Real-Time Path Integral Simulation of Energy Transfer in Light Harvesting Complexes”
10:00-10:20 Océane Mangel, Université Grenoble Alpes, “Study of the Streptomyces tyrosinase reaction mechanism: a dynamic QM/MM approach”
10:20-11:00 Coffee Break
11:00-11:30 Fahmi Himo, Stockholm University, Sweden, “Mechanism of Vanadium Chloroperoxidase from Quantum Chemical Calculations”
11:30-11:50 Sergio Sousa, University of Porto, Portugal, “Probing the Role Played by Different Amino Acid Residues in the Catalytic Mechanism of Plastic PET degrading by QM/MM Methods”
11:50-12:10 Jon Uranga, University of the Basque Country, Spain, “A Lysine-Cysteine Redox Switch: The NOS Bridge”
12:10-12:.30 Elise White, University of Bristol, UK, “Multi-scale simulations provide insights for engineering product outcome of polyketide synthases”
12:30-14:00 Relocation from the Academy of Athens to the Biomedical Research Foundation with buses

Lunch at BRFAA

14:00-1600 Biomolecular Dynamics II

Chair: Annick Dejaegere

14:00-14:30 Nigel Richards, Cardiff University, UK, “Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase”
14:30-15:00 Themis Lazaridis, City College of New York, USA, “Classical simulations with proton transfer: insights into proton channels”
15:00-15:30 Sophie Sacquin-Mora, CNRS, France, “Investigating the dynamics of protein-protein interfaces in well structured and fuzzy complexes
15:30-16:00 Matthias Buck, Case Western Reserve University, USA, “Learning to use AlphaFoldMultimer and variants – amazing to not so good for transmembrane proteins”
16:00-16:30 Coffee Break
16:30-17:15 Loew Lectureship

Chair: Zoe Cournia

Kennie Merz, Michigan State University, USA ,Transition Metal Modeling in Aqueous Solution”
17:15-17:30 Nigel Richards, Cardiff University, UK, “Remembering Peter Politzer”
17:30-20:00 Poster Session
Wednesday 22 May 2024
Biomedical Research Foundation, Academy of Athens (BRFAA)
09:00-12:40 Computer-aided drug design

Chair: Evi Gkeka

09:00-09:30 José Duca, Novartis Institutes of Biomedical Research, USA, “Modeling the undruggable; from the computer to the clinic”
09:30-10:00 Marco De Vivo, Italian Institute of Technology, Italy, “Targeting the conserved active site of splicing machines”
10:00-10:30 Thomas Mavromoustakos, University of Athens, Greece, “Computational Analysis and Drug Discovery”
10:30-11:00 Coffee Break
11:00-11:20 Minos Matsoukas, University of West Attica, Greece, “Computational approaches in targeting GPCRs and cancer related proteins with small molecules”
11:20-11:50 Serdar Durdagi, Bahçeşehir University, Turkey, “Development of New Virtual Screening Methods Incorporating Artificial Intelligence Approaches to Accelerate the Transition from Preclinical to Clinical Stages in Drug Development”
11:50-12:20 Manos Mikros, University of Athens, Greece, “In silico tools for the discovery and optimization of new bioactive compounds”
12:10-12:.40 Özge Kürkçüoglu, Instabul Technical University, Turkey, “In Silico Identification of Allosteric Sites and Modulators on GPCRs Using Residue Network Model and Site Identification by Ligand Competitive Saturation”
12:40-14:00 Lunch Break and Poster Session
14:00-17:30 Nucleic Acids Modeling

Chair: Thomas Cheatham

14:00-14:30 Modesto Orozco, University of Barcelona, Spain, “Frontiers in molecular dynamics of nucleic acids”
14:30-15:00 Evi Gkeka, Sanofi, France, “Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN”
15:00-15:20 Nathalie Basdevant, Université d’Evry Paris Saclay, France, “DNA translocation through alpha-hemolysin nanopore using the MARTINI coarse-grained force field”
15:20-15:40 Maxime Kermarrec, Ecole Normale Supérieure de Lyon, France, “Mapping the Radical Cation Guanine in the nucleosomal DNA using QM/MM approaches”
15:40-16:00 Coffee Break
16:00-16:30 Alessandra Magistrato, Trieste SISSA, Italy, “Molecular Mechanisms of RNA Metabolism”
16:30-17:00 Vlad Cojocaru, Universitatea Babes-Bolyai, Romania, “Transcription factors meet chromatin under the computational nanoscope”
17:00-17:30 Sarah Harris, University of Leeds UK, “Multi-Scale Simulations of DNA Supercoiling”
17:30-18:05 Flash Talks

Chair: Klaus Liedl

Isidora Diakogiannaki, University of Naples Federico II, Italy, “Modeling A40s Aptamer for Advancing Glioblastoma Therapy”
Petr Jurečka, Palacky University Olomouc, Czech Republic, “Developing Force Field for Nucleic Acids Simulations – Both Canonical and Non-canonical”
Gianfranco Martino, University of Bologna, Italy, “MD simulatons identify precise and dynamic protein cooperation for the spliceosomal splicing”
Fethiye Aylin Sungur, Istanbul Technical University, Turkey, “A Multiscale Modelling Study to Elucidate the Citrullination Reaction of the Protein Arginine Deiminase 2 and Identifying New Hit Compounds”
Roxana Geanina Vasarhelyi, Babes-Bolyai University, Romania, “Exploring RNA-protein interactions: from binding modes to sequence specificity through molecular docking and simulations“
Alessia Visigalli, Italian Institute of Technology, Italy, “Molecular Dynamics Simulations to study translocation in Human DNA Polymerase”
Merve Yuce, Istanbul Technical University, Turkey, “Identification of Potent E. coli Ribosome Inhibitors Using a Computationally Efficient Workflow”
18.05-19:30 ISQBP Business Meeting
20:30 Conference dinner
Thursday 23 May 2024,
Biomedical Research Foundation, Academy of Athens (BRFAA)
09:00-11:00 Biomolecular dynamics and drug discovery

Chair: Minos Matsoukas

09:00-09:30 Andrea Cavalli, CECAM, Switzerland, Physics-based approaches to computational drug discovery
09:30-10:00 Vangelis Daskalakis,University of Patras, Greece, “CRISPR-Cas proteins: Engineering of “silver-bullets” in the arsenal of gene editing”
10:00-10:20 Nishita Mandal, Adam Mickiewicz University, Poland, “Probing Ligand Transport Pathways in Proteins with Buried Active Sites: Insights from Coarse-Grained Molecular Dynamics Simulations”
10:20-10:40 Giulia Paiardi, Heidelberg University, Germany “The role of heparin in spike SARS-COV-2 infection: From a model for heparan sulfates to a starting structure for antivirals”
10:40-11:00 Alexios Chatzigoulas, Biomedical Research Foundation, Academy of Athens, Greece, “Predicting protein-membrane interfaces of peripheral membrane proteins using AI”
11:00-11:30 Coffee Break
11:30-12:40 Force Field Development

Chair: Zoe Cournia

11:30 – 12.00 Adrian Roitberg, University of Florida, USA, “Machine Learning Potentials for Molecular Modeling. ANAKIN, The Next Generation”
12:00-12:20 Franz Waibl, ETH Zürich, Switzerland, “Validating small-molecule force fields for simulation of macrocycles”
12:20-12:40 Panagiotis Koukos, Biomedical Research Foundation, Academy of Athens, Greece, “Martini 3 force field parameters for protein lipidation post-translational modifications”
12:40-12:50 Best talk and poster awards
12:50 Closing remarks and farewell – End of Conference