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Today an update to simbols (gitlab.uni-oldenburg.de/quantbiolab/si…) went online and onto PyPI. It should now be more accessible to different operating systems and can be installed again through pip as the interaction with a dependency has been fixed. :-)

Looking forward to 2 days of advanced methods in molecular dynamics simulations Kongelige Danske Videnskabernes Selskab. Talks by Erik Lindahl - eriklindahl.bsky.social, Syma Khalid, Anna Duncan, Max Bonomi, Roberto Covino, Weria Pezeshkian. Organised by @chrisjorg_1, Himanshu Khandelia, Birgit Schiøtt Biomodelling Aarhus Uni & myself mdmeeting2023.wordpress.com

We are happy to introduce our latest program ALISE- the Automated Ligand Searcher, which was made possible because of the great collaborative effort of Fabian Luise Jacobsen Jonathan Hungerland. pubs.acs.org/doi/full/10.10…

Introducing the Automated Ligand Searcher #DrugDiscovery pubs.acs.org/doi/10.1021/ac… Luise Jacobsen Jonathan Hungerland Fabian QuantBio Group #JCIM Vol63 Issue23 #compchem

I have an open PhD position. If you are looking for a biomoldeing PhD position, this is for you. candidate.hr-manager.net/ApplicationIni…

We used Siewert-Jan Marrink to simulate 700 microseconds of protein dynamics. I'm very glad the study is out. We even won the cover art. Check out the supplementary videos as well :-)

Got back from the DGfB's International Membrane Biophysics Meeting "From Model to Cellular Membranes". A fun meeting, one of the best poster sessions I have attended so far and a pretty location. Three of Weria Pezeshkian's group joined, Neda, Adrià and me (right to left)

Our article was published in #moleculardiversity, available at rdcu.be/dHQOJ! With Felicitas Finke, Jonathan Hungerland, and QuantBio Group, we discuss how receptor structures built with SWISS-MODEL or #AlphaFold behave in #drugscreening for the tick-born #encephalitis virus.

iopscience.iop.org/article/10.108… A very fun project reached its conclusion in this latest published manuscript. With Jonathan and QuantBio Group, we look at and utilize the (surprising) negative eigenvalues in positiv semi-definit matrices :). Check it out!

Yesterday, I presented a talk entitled "Experimental data informs molecular cluster prediction in mitochondria" at ECMTB 2024. Thanks for listening and the picture taken from the audience.

Register for our workshop on molecular modeling. Unfortunately, the number of seats is limited. indico.nbi.ku.dk/event/2076/

Physical Chemistry Teachers: We just published our protocols for a computer laboratory for calculating the heat capacity of the unfolding of a peptide, which we use in a large Bachelor level course. bit.ly/3Apu2rJ.

Combining activity assays, molecular dynamics, and networks, we (QuantBio Group,Alice Wong) uncover chemical information pathways across multiple domains in GC-E protein. Important residues match mutation sites that induce various diseases and blindness. Tinyurl.com/pathsgce

Balcony poster session overlooking the city in nice weather at the ISBUC innovation day 2024 today. Had a good time. 😀

We looked at the potential energy that guides molecular dynamic simulations to derive nuanced intra-protein pathways and potentially recover and suggest mutation sites. I'm very happy this was published. For me, it was/is a fun and exciting project.

In this latest study, Fabian, H. Bordallo, and Weria Pezeshkian leverage the potential energy that guides molecular dynamics simulations to inform allosteric networks and recover known mutation sites in Cathepsin G and Neutrophil Elastase. go.acs.org/bbc

PhD position // University of Oldenburg uol.de/en/job/phd-pos…

Can we use cross-linking mass spectrometry data to construct mesoscale simulations with predictive power? Check out our recent paper in Angewandte Chemie, and congratulations to my postdoc Fabian and all the other authors onlinelibrary.wiley.com/doi/10.1002/an…

It was even marked as a "very important paper". Very happy about this development

New preprint: TS2CG v2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion. biorxiv.org/content/10.110… Siewert-Jan Marrink Source code: github.com/weria-pezeshki…