Thor van Heesch

Super excited to share together with @jocelyne_vreede and Peter Bolhuis my first research paper published in Nucleic Acids Research! We have developed a molecular simulation approach for predicting dissociation free energies of protein-DNA complexes:

Monte Carlo with expanded ensembles are powerful methods to compute adsorption and diffusion processes in nanoporous materials. In @JChemPhys , we present RASPA3, the new version of the RASPA2 code. (1/8) pubs.aip.org/aip/jcp/articl…

~2 weeks left to apply! Thanks for your interest & RTs.

🚨 Hiring! Looking for a motivated #PhD student to work with me on molecular #simulations and #machinelearning to predict #nanoplastic risks to #protein function. Further details: vacatures.uva.nl/UvA/job/PhD-in… RT appreciated #compchem #softmatter @jobRxiv @HimsUva @UvA_Science

🔬 Happy to announce our latest publication "Unlocking Novel Therapies: Cyclic Peptide Design for Amyloidogenic Targets through Synergies of Experiments, Simulations, and Machine Learning." 📚 #AmyloidogenicTargets #ML #CyclicPeptideDesign shorturl.at/yPX79

@olexandr I ran into the same issue a while ago, maybe this could be of use: github.com/Heezch/capper

Hey #compchem hivemind pracical question. I have pdb file with multiple chains. Any easy to run script that can go over chains and cap each end with ACE/NME without causing substantial clashes?

For more in-depth insights and detailed methodology, check out our full paper in @NAR_Open doi.org/10.1093/nar/gk…

Our method's versatility extends beyond minor groove binders like H-NS. It's equally effective for major groove binding proteins. We applied our technique to a major groove binder, the ETS domain of the PU.1 TF. Again, we were able to identify the consensus sequence correctly!

Super excited to share together with @jocelyne_vreede and Peter Bolhuis my first research paper published in Nucleic Acids Research! We have developed a molecular simulation approach for predicting dissociation free energies of protein-DNA complexes:

Hello @IUPAC2023! Today at 10:20, during the #Chemistry & #AI session, I will present our work with @thorvanheesch & @BerndEnsing from @CompChemUvA @HimsUva @UvA_Science on finding molecular descriptors from (meta)stable-state data :)

I made a free addon for pixel art rendering with blender! full tutorial and download link: lucasroedel.gumroad.com/l/pixel_art #blender #b3d #pixelart

@HansScholl42 @bradyajohnston @openmm_toolkit For DNA you could also look at worm-like chain models, or oxDNA (if that is also on your radar)

@HansScholl42 @bradyajohnston @openmm_toolkit I was also thinking about CG! But then you have to do the back-mapping step, which can be tricky (especially for somewhat smooth animations) But if you feel like trying either way, Martini or the AWSEM protein coarse grained force fields are pretty good! github.com/npschafer/open…

is this molecular dynamics 🤔🤔

@bradyajohnston @HansScholl42 Have a look at @openmm_toolkit it’s a MD engine with a very nice python api

@HansScholl42 The addon can read trajectory files, so I can already playback properly computed MD trajectories. I'm just trying to get working a _very_ rough atomistic solver that could be used for quick visualisation purposes. Geometry Nodes is C++ so it's ~~relatively~~ quick (sadly not GPU)

🚨Looking for 2 postdocs to join @UvA_Science @ai4science_lab 4 sustainable molecules & materials! Salt hydrates 4 thermal storage (with Shahidzadeh, Woutersen) Plant proteins 4 sustainable food (Bolhuis, van Hoof, Jabbari-Farouji, Quattrocchio, Schall) vacatures.uva.nl/UvA/job/4-Post…

🚨 Hiring! Looking for a motivated PhD student to work with me on automated computational design of molecules & soft materials for sustainability & health. Further details: vacatures.uva.nl/UvA/job/PhD-in… Retweets appreciated #compchem #softmatter @Chemjobber @jobRxiv

@bradyajohnston Just sent you a PM!

@thorvanheesch Ooh would be very interested in this if you are willing to share!

I'm after any molecular dynamics simulation data for some upcoming talks / videos. Can anyone help me out? I'm currently after ideally a simulation showing ions passing through an ion channel. Ideally lots of time steps, lots of atoms (waters, ions, EVERYTHING)