Original post on social.edu.nl

Two papers for the ICCS Collection in the Journal of Cheminformatics have been tagged as accepted now. With another 4 under review, and at least one more paper to be submitted. The deadline was extended one last time.

But we are looking forward to a nice collection of work presented at the ICCS […]

Research from the 13th International Conference on Chemical Structures The 13th International Conference on Chemical Structures (ICCS 2025) will take place on June 1-5, 2025, in Noordwijkerhout, The Netherlands, where it has been ...

The submission deadline for the ICCS Collection in the Journal of Cheminformatics will be extended to March 1. We currently have four papers under review and expect at 2 more submissions.

https://link.springer.com/collections/jcfcedbfda

#cheminformatics #iccs2025

Posters – ICCS

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

Sano at #ICCS2025 🇸🇬
Highlights: AI for drug discovery, Cloud RNA-seq (23% faster!), Human connectome at nanoscale, 3D vein modeling, Connecting with global experts on scalable biomedical infrastructure
💡The future of medicine runs on code.
#ComputationalScience #AI #Neuroscience #CloudComputing

Graph depiction with five articles as nodes with the article titles as node labels, and edges between them based on CiTO intent annotations. We see two research papers, resulting in three "letters to the editor" creating a lively discussions with scientific critiques going back and forth. The graph can be recreated with this SPARQL: https://w.wiki/EYE5

scientific discussion moved from "letters to the editor" to PubPeer. There is a lot to be said about that, but one thing that must be said is that PubPeer can disappear.

But Letters to the Editor are preserved, for better or worse. if not mistaken, it was […]

[Original post on social.edu.nl]

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: chem-bla-ics.linkedchemistry.info/2025/06/08/iccs2025-1-ba...

#iccs2025

Scientific program – ICCS

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: iccs-nl.org/general-information/scie...
- 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

ORCID

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?"

ORCID

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

ORCID

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

ORCID

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

ORCID

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

Original post on social.edu.nl

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 […]

ORCID

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

Screenshot of the linked WikiPathways, showing at the top various ETR1 variants and the downstream signalling.

@intconfchemstr also happy to see the ETR1 signalling pathway is at least for one species (not fruit) in @wikipathways: https://www.wikipathways.org/pathways/WP2851.html

#ICCS2025

@intconfchemstr interesting aspect of this work was that the binding of agonists and antagonists of fruit ripening involves the binding with the copper ion in ETR1. The orientation of the HOMO/LUMO in the active site seems to correlate (determine) the biological action

#ICCS2025

ORCID

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

ORCID

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

DockM8 - Home ​DockM8 is an all-in-one open-source Structure-Based Virtual Screening workflow based on consensus docking. It handles library preparation, docking, clustering of docking poses, rescoring and consensus ranking.

Lacour is presenting the #opensource DockM8: https://drugbud-suite.github.io/dockm8-web/

#ICCS2025

ORCID

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

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"

ORCID

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

Original post on social.edu.nl

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 […]