ICCS

six #ICCS2025 posters can now be download from our website at https://iccs-nl.org/posters/

A fediwall for #ICCS2025, two other tags, and this account. It shows posts with those tags, e.g. from @dalke@toots.nu and @egonw@social.edu.nl

fediwalls are a thing! just 3 weeks too late for #ICCS2025

ICCS2025: back in Noordwijkerhout This week the 13th International Conference on Chemical Structures took place (see also this Scholia overview or this overview of the full ICCS history). This is the conference I first joined 20 years ago as a PhD student presenting a poster (see these past blog posts). Of course, I am actually co-organizer nowadays (actually, co-treasurer). Organizing a meeting with just over 200 participants, and I like to thank Gerard and Willem in particular, but also Pieter, Marcus, Frank, Jenke, and Frans Koeman who has helped us during the past three events. The meeting started, as usual, wth the CSA Trust Mike Lynch Award, this year awarded to Prof. Val Gillet (see also this press release). This time, there where the following themes, where the first was by far the most dominant theme: * Artificial Intelligence, Machine Learning, and QSAR (five sessions) * New Modalities and Large Chemical Data Sets (one session) * Advanced Cheminformatics Techniques (two sessions) * Integrative Structure-Based Drug Design (two sessions) My contribution this time was a poster for the VHP4Safety project, but more about that later. Like last time, I have been annotating speakers with identifier and accounts, if they provided those: As you can see, it also includes PDFs, for both talks and posters. At the time of writing, I collected PDFs of two presentations and five posters. Additions are still most welcome, ideally with DOI, so that they can be cited (doi:10.5281/zenodo.15494630, doi:10.13140/RG.2.2.27441.90720 doi:10.5281/zenodo.15614295, and doi:10.13140/RG.2.2.36774.23365)! Finally, I like to remind everyone that there is again a proceedings collection in the Journal of Cheminformatics, and presenters of oral and poster presentations are invited to submit their presented work to this collection.

I wanted to blog more, but there was too busy during the day. So, I have so far only this: https://chem-bla-ics.linkedchemistry.info/2025/06/08/iccs2025-1-back-in-noordwijkerhout.html

#iccs2025

and don't forget to cite the DOI for those that have them

if you missed the #ICCS2025, you can catch up with the slidedeck and poster PDFs that presenters have made available online, and counting:

- 1 presentation: https://iccs-nl.org/general-information/scientific-program/
- 4 posters: https://iccs-nl.org/posters/

Photo of Gerard van Westen on stage and the "Save the Date!" slide announcing ICCS 2028, from June 11th to June 15th and the hashtag for that meeting: #ICCS2028

the next International Conference on Chemical Structures, edition 14, will be held in the week of June 11-15 2028!

#ICCS2025 #ICCS2028

and there we are! the final #ICCS2025 talk!

Philipp Janssen (https://orcid.org/0000-0003-3223-9182) of University of Münster is answering in his talk "How unsociable is the fragment space, and can we do better?"

the third talk is by Niklas Piet Doering (https://orcid.org/0009-0004-8238-2985) from Freie Universität Berlin, with a talk about "MDPath: Unraveling Allosteric Communication Pathways through Molecular Dynamics Simulations"

#ICCS2025

we continue with Andreas Göller from Bayer AG, with the talk "Quantum Mechanics for Ligand Design, Binding Affinities, Toxicity Risk and Process Chemistry: Successes and Obstacles"

#ICCS2025

the last session has just started. First presentation is by Henriette Willems (https://orcid.org/0000-0001-7196-5975) from the University of Cambridge, with her talk "How useful are protein folding tools for drug design?"

#ICCS2025

now talking the floor is Domen Pregeljc (https://orcid.org/0009-0009-6310-904X) from ETH Zurich on "Advancing free-energy calculations by combining multiscale modeling and multistate enhanced sampling"

#ICCS2025

and this session was concluded by a talk by James Webster (https://orcid.org/0000-0002-7014-6350) of University of Dundee, on "Modernising the Reaction Vector Framework: From Legacy Code to Validated Synthesis"

#ICCS2025

the third talk was by Bernardo de Souza from FACCTs GmbH on "Validating the prediction of lowest-energy tautomers and conformers against experimental techniques"

#ICCS2025

the second talk in this session was Andrius Bernatavicius from Leiden University, with the talk title: "Docking-based geometric graph models for kinase-ligand affinity prediction"

#ICCS2025

yesterday, after the coffee break, we had four talks. The session was kicked of by John Wilkinson Mayfield (https://orcid.org/0000-0001-7730-2646) of NextMove Software showing even faster substructure search on billion-sized compound sets in "Honey, I shrunk the database: Making multi-billion […]

next speaker is Leon Moritz Obendorf (https://orcid.org/0000-0002-5641-4961) from the Freie Universität Berlin. This talk has the title: "AI and MD-aided computational docking pipeline to elucidate TGF-beta type l receptor & signaling mediator interaction"

#ICCS2025

and the final talk before the coffee break was by Luke Rossen (https://orcid.org/0009-0008-4942-0360) from the Eindhoven University of Technology on "Scaffold Hopping with Generative Reinforcement Learning"

#ICCS2025

the second talk yesterday was given by Rafał Adam Bachorz from Simulations Plus on :Navigating Synthon Space: Property-Driven Molecular Optimization for Pharmacokinetics"

#ICCS2025

Yesterday, the first session had three talks, starting with Afnan Sultan (https://orcid.org/0009-0000-6126-7153) from Saarland University with the talk: "Transformers for molecular property prediction: Domain adaptation efficiently improves performance"

#ICCS2025

the second speaker is Lisa Sophie Kersten from Heinrich Heine University with the talk"Computational Challenges in Modeling Metal-Binding Sites in Proteins: A Multiscale Approach to Copper-Ligand Interactions in the Plant Receptor ETR1"

#ICCS2025

Thursday morning is the last stretch of the meeting. First speaker is Antoine Michel Lauder Lacour (https://orcid.org/0000-0002-0051-8710) from Saarland University. The title of his talk is "DockM8: All-in-One Open-Source Platform for Consensus Virtual Drug Screening"

#ICCS2025

yesterday, we did not manager to put up the presenter names and talk titles, but we'll do so shortly. and in the afternoon, we had out social event, so you did not miss many.

where the sessions on Monday and yesterday morning were about "Artificial Intelligence, Machine Learning, and QSAR", yesterday afternoon was about "New Modalities and Large Chemical Data Sets"

Today's two sessions are about the third #ICCS2025 theme: "Advanced Cheminformatics Techniques"

the final talk today is by Torben Gutermuth (https://orcid.org/0000-0002-9304-8251) of University of Hamburg, with the talk: "StrAcTable – Combining Structural and Bioactivity Data with Atomic Precision for Protein-Ligand Complex Datasets"

#ICCS2025

now speaking is Christoph Steinbeck (https://orcid.org/0000-0001-6966-0814) from Friedrich-Schiller-University Jena: "COCONUT 2.0: A Comprehensive Improved Open Database for Natural Products Research"

His slides can be found at […]

second speaker is Modest von Korff (https://orcid.org/0000-0002-2549-8672) from Alipheron AG. The title of the talk is "Benchmarking Searching in Combinatorial Spaces with the Approved Drug Space"

#ICCS2025

third session today starts with a presentation by Olga Tarkhanova (https://orcid.org/0000-0003-1880-2872) from Chemspace LLC: "A Workflow Pairing Rational and Computational PROTACs Design Yields a Novel BRD4 Degrader"

#ICCS2025

second talk is given by Aya Abdelbaky from Pangea Bio, with the title "SpectruMS: A Multi-modal Foundation Model for Better Generalizability on Tandem MS2 Data"

#ICCS2025

the second session now starts with the talk "Discovery of Novel CYP19A1 Inhibitors Using Machine Learning-Driven Virtual Screening and Structure-Based Approaches", by Sijie Liu (https://orcid.org/0000-0001-8834-3881) from the Freie Universität Berlin

#ICCS2025

third speaker before the coffee break is Pavel Polishchuk (https://orcid.org/0000-0001-5088-8149, https://github.com/ci-lab-cz, and https://github.com/DrrDom) from Palacky University, with the talk: "CACHE Challenge #1: Searching for Hit Molecules in Ultra-Large Chemical Libraries Guided By De […]