35th Molecular Modelling Workshop 2023 MGMS-DS e.V. Logo
35th Molecular Modelling Workshop 2023

Program: Monday, March 13th 2023
11:00 - 14:00
Registration (Chemikum)
14:00 - 14:10
Welcome remarks / Agenda review
14:10 - 14:35
L5: Conrad Hübler, TU Freiberg
The Hungarian method revisited - Usage of combinatorial optimisation for structural comparison of conformers
14:35 - 15:00
L2: Filipe Menezes, Helmholtz Institut München
A Semi-Empirical Energy Decomposition Analysis for large (Bio)Molecular Systems
15:00 - 15:50
Plenary 1: Paolo Carloni, FZ Jülich
MiMiC: A new, highly scalable QM/MM interface for biophysical applications
15:50 - 16:30
Coffee break
16:30 - 16:55
L3: Jacqueline C. Calderon, CCC, FAU Erlangen
The structural basis that drives ligand efficacy at the serotonin 5-HT1A receptor
16:55 - 17:20
L4: Hebah Fatafta, FZ Jülich
Dissecting Membrane-Amyloid Peptide Interactions at the Atomic Level: Insights from Peptide Monomers and Oligomers
17:20 - 17:45
L1: Simone Bonfrate, Aix-Marseille University
Simple and efficient electrostatic embedding QM/MM method for modelling condensed phases using periodic boundary conditions
18:00 - 19:00
Annual Meeting of the MGMS-DS e.V.
Buffet - Dinner


Program: Tuesday, March 14th 2023
09:00 - 09:25
L6: Benedikt Frieg, FZ Jülich
Interdisciplinary insights into the influence of lipids on the formation of alpha-synuclein fibrils in Parkinson’s disease
09:25 - 09:50
L7: Rocco Gentile, Heinrich-Heine-Universität Düsseldorf
Molecular mechanisms underlying the activity regulation of the phospholipase PlaF from P. aeruginosa by free fatty acids
09:50 - 10:15
L8: Anna Jäckering, FZ Jülich
Engineering PET-degrading enzymes - targeting the energy barrier for PET binding
10:15 - 10:55
Coffee break & Conference photo
10:55 - 11:20
L9: Aswathy Muttathukattil, FAU Erlangen
Self-limiting Assembly in Systems of Bipods via Geometrical Frustration
11:20 - 12:10
Plenary 2: Markus Reiher, ETH Zürich
Prospects of Quantum Computing for Chemistry
12:10 - 13:30
13:30 - 15:00
Poster Session
15:00 - 15:25
L10: Lisa Sophie Kersten, Heinrich-Heine University Düsseldorf
Structural dynamics in plant receptor ETR1 after binding of ethylene and 1-methylcyclopropene
15:25 - 15:50
L11: Fabian Sendzik, TU Dortmund
Localization and decomposition of free energies in solution
15:50 - 16:10
Coffee break
16:10 - 16:35
L12: Marius F. W. Trollmann, FAU Erlangen
mRNA lipid nanoparticle phase transition
16:35 - 17:00
L13: Joana Massa, Universität Münster
Metadynamics Simulations of FPR2: Using an Enhanced Sampling Method to Elucidate The Mode of Action of a Diverse Set of Ligands
17:00 - 17:25
L14: Frank Beierlein, NHR@FAU Erlangen
DNA Repair Mechanisms: Molecular Simulations and Computational Alchemy
17:25 - 18:15
Plenary 3: Peter Hildebrand, Universität Leipzig
Structural mechanism of Gs protein activation by the prototypical beta-2 adrenergic receptor
MMWS Social Event @ Kitzmann Brauschänke, Südl. Stadtmauerstr. 25, 91054 Erlangen


Program: Wednesday, March 15th 2023
Topic: HPC meets Molecular Modelling
09:00 - 09:25
L15: Gerhard Wellein, NHR@FAU Erlangen
The National High-Performance Computing Alliance: New infrastructure and opportunities for science and research at German universities
09:25 - 09:50
L16: Alireza Ghasemi, NHR@FAU Erlangen
Machine Learning Interatomic Potentials: Reference Training Data on the Hands of Workflows
09:50 - 10:40
Plenary 4: Oliver Koch, Universität Münster
Neural Fingerprints: Structure- and activity-sensitive molecular representations based on neural networks for virtual screening approaches
10:40 - 11:10
Coffee break
11:10 - 11:35
L17: Anna Bochicchio, Schrödinger GmbH München
Enabling Prediction of Protein-Protein Binding Affinities Using FEP+
11:35 - 12:00
L18: Christian Ritterhof, ICMM and CCC, FAU Erlangen
Accelerating plane wave based ab initio molecular dynamics by optimization of Fast-Fourier transforms for modern HPC architectures
12:00 - 12:25
L19: Julian Konrad, CCC, FAU Erlangen
Multi-Scale Modelling of Epoxy Resin and Composites: from Curing to Fracture
12:25 - 12:50
L20: Nicolas Tielker, Patrick Kibies, TU Dortmund
Recent advances in the Embedded Cluster Reference Interaction Site Model
12:50 - 13:15
Poster & Lecture awards, Closing & Good Bye



Poster Session: Tuesday, March 14th 2023, 13:30 - 15:00
Jorge Antonio Amador Balderas,
FAU Erlangen
Effect of N140D and T197A mutations on DNA repair enzyme Thymine DNA Glycosylase
Anton Arkhypov,
FAU Erlangen
Optimisation of electrophile reactivity
Frank Beierlein,
NHR@FAU, CCC, FAU Erlangen
DNA-Repair Mechanisms: Molecular Simulations and Computational Alchemy
Jacqueline Calderon,
FAU Erlangen
The structural basis that drives ligand efficacy at the serotonin 5-HAT1A receptor
Marcus Conrad,
FAU Erlangen
Mechanics of Histamine: Computational analysis of protonation effects on H1R binding
Maximilian Dejori,
FAU Erlangen
Quantum chemical analysis of structure and ion selectivity correlation of moieties derived from the [2.2.2] cryptand
Manuel Deubler,
FAU Erlangen
Structure-based design and optimization of ligands for novel antiviral strategies
Steffen Docter,
FZ Jülich
Amine Transaminase Engineering based on Constraint Network Analysis
Rustam Durdyyev,
FAU Erlangen
Modelling liquid flow through nanopores on the nanoscale
Lennart Eisel,
TU Dortmund
Accurate prediction of acidity constants with an ONIOM embedded cluster RISM approach
Jules Cesar Epee Ndongue,
FAU Erlangen
Towards automated exploration of enzymatic reactions
Federico Tomazic,
FAU Erlangen
Coarse-Grained Simulations of Ligand-Tethered Nano-Tripods
Lars Schumann,
TU Dortmund
Identifying descriptors of the conductive state in small viral K ion channels
Anselm Horn,
FAU Erlangen
Count on NHR@FAU for your Atomistic Simulations
Stephen Hummel,
Boston College / US Army
digitalSELEX: In silico Platform for Designing Oligonucleotides
Eileen Socher,
FAU Erlangen
Molecular Case Study of a GALC Mutation Causing Infantile Krabbe Disease
Patrick Kibies,
TU Dortmund
Recent advances in the Embedded Cluster Reference Interaction Site Model
Azad Kirsan,
FAU Erlangen
Metadynamics Simulations of Chemical Reactions in Solution
Joana Massa,
Universität Münster
KCa3.1 channel: Computational analysis of three known toxin inhibitors towards new extracellular inhibitors
Stefan Maste,
TU Dortmund
Accurate NMR shift calculations for species in aqueous solution at ambient and high-pressure conditions
Debora Monego,
HITS Heidelberg
Size-dependent sedimentation of nanocrystals: the role of the ligand shell structure
Nathaniel Smith,
A combined deep learning and structure based cheminformatic approach to understand ligand blockage activity on the hERG channel
Christian Ritterhoff,
FAU Erlangen
Accelerating plane-wave-based ab initio molecular dynamics by optimization of Fast-Fourier transforms for modern HPC architectures
Simon Schäfer,
FAU Erlangen
Unlocking the Potential of Antibodies Against SARS-CoV-2: A Pipeline for Fast and Accurate Mapping of Interaction Sites with Free Energy Analysis
Felix Bänsch,
Westphalian University of Applied Sciences
A Calculation Pipeline for Differential Molecule Pair Interaction Energies
Felix Bänsch,
Westphalian University of Applied Sciences
MORTAR – A Rich Client Application for in silico Molecule Fragmentation; A Calculation Pipeline for Differential Molecule Pair Interaction Energies



The following event may also be interesting for you: The NHR@FAU Colloquium starts one hour after the Molecular Modelling Workshop at the same location. If your schedule permits, consider to stay a bit longer in Erlangen and learn about the HPC services provided by the Erlangen National High Performance Computing Center (NHR@FAU).


NHR@FAU Symposium
This meeting is free of charge, but registration is necessary. If you are interested in participating, please see the information provided below.
Program: Wednesday, March 15th 2023
NHR@FAU Colloquium: Celebrating Two Years of National HPC Service
Welcome addresses, invited talks, guided tours, reception. More details are available on the corresponding web pages.


Program: Thursday, March 16th 2023
NHR@FAU Results Symposium
Scientific presentations (with lunch and coffee break). More details are available on the corresponding web pages.