MolDyn group Freiburg @MolDynFR
Twitter of the Stock lab at the Albert-Ludwigs University Freiburg. Biomolecular Dynamics, nonequilibrium, dimensionality reduction, machine learning. moldyn.uni-freiburg.de Freiburg, Germany Joined January 2020-
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And that's a wrap for our RU-workshop "Reducing complexity of nonequilibrium systems"! A heartfelt thank you to all speakers and participants for making this meeting a success! And here some pictures of some serious efforts at barrier crossing and pathway sampling while hiking!
Newest work from us on reweighing biased data from dcTMD simulations in protein conformational transitions & obtaining their kinetics! Just in time for the @for5099 workshop!
Newest work from us on reweighing biased data from dcTMD simulations in protein conformational transitions & obtaining their kinetics! Just in time for the @for5099 workshop!
Our group is joining the workshop of the @for5099, including presentations by Gerhard, @sofii_sarto, @die_jaegerIn and @Herr_Flow!
Our group is joining the workshop of the @for5099, including presentations by Gerhard, @sofii_sarto, @die_jaegerIn and @Herr_Flow!
Newest work from us including @sofii_sarto and @gegadiez : Toward a Benchmark for Markov State Models: The Folding of HP35. Out now in @JPhysChem Letters #compchem pubs.acs.org/doi/10.1021/ac…
Newest work from us by Daniel Nagel and @sofii_sarto , a Perspective on providing a benchmark model for Markov State Models on protein folding: arxiv.org/abs/2306.04331
Our now in JOSS: an application note for msmhelper, a Python package for Markov state modeling of protein dynamics that Daniel Nagel developed in our group! #compchem
Our now in JOSS: an application note for msmhelper, a Python package for Markov state modeling of protein dynamics that Daniel Nagel developed in our group! #compchem
Our article on anisotropic friction in @NanoLetters has made it to the Cover of the Journal! Props to @die_jaegerIn for the Cover art (I'm really happy that the introduction to Blender seminar I gave in the @MolDynFR group is bearing fruit)! pubs.acs.org/toc/nalefd/23/…
New work from Daniel Nagel and @sofii_sarto : We rigorously analyze the strengths and drawbacks of different input features for dimensionality reduction, the structural information of the resulting clusters, and the information content of the final MSMs. pubs.acs.org/doi/10.1021/ac…
New work from our @die_jaegerIn and @Herr_Flow in collaboration with @HugelLab and @BalzerBizan on how friction is an anisotropic property within protein-ligand systems! #FOR5099
New work from our @die_jaegerIn and @Herr_Flow in collaboration with @HugelLab and @BalzerBizan on how friction is an anisotropic property within protein-ligand systems! #FOR5099
Finally out in @NanoLetters: Anisotropic Friction in a Ligand-Protein Complex. A great collaboration between W. Cai, @HugelLab and @BalzerBizan at @UniFreiburg, J. T. Bullerjahn at @MPIbp, while @die_jaegerIn and I did the MD simulations. #compchem pubs.acs.org/doi/10.1021/ac…
Newest work from us on parameterising Langevin fields for ligand (un)binding simulations along several pathways and combine the result into a global rate. Out now in JCP as Editor's pick! #FOR5099
Newest work from us on parameterising Langevin fields for ligand (un)binding simulations along several pathways and combine the result into a global rate. Out now in JCP as Editor's pick! #FOR5099
Final work from us this year: Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding. Available now at arxiv.org . #compchem
Out now in @JPhysChem B with Nadja Helmer and @Herr_Flow: Energy Transport and Its Function in Heptahelical Transmembrane Proteins. We find that bacteriorhodopsin has a "lightning rod" for excess photon energy, while rhodopsin is bad at releasing energy. pubs.acs.org/doi/10.1021/ac…
Our work together with Ahmed Ali, @AG78617 and @Herr_Flow on Nonequilibrium Modeling of the Elementary Step in PDZ3 Allosteric Communication is now out in @JPhysChem Letters: pubs.acs.org/doi/10.1021/ac…
New work from @SimonBray18 , Victor Tänzel and @Herr_Flow from our group on how to cluster not states, but trajectories to reveal pathways between states and to find the respective reaction coordinates of relevance using ML and Neighbour-nets.
New work from @SimonBray18 , Victor Tänzel and @Herr_Flow from our group on how to cluster not states, but trajectories to reveal pathways between states and to find the respective reaction coordinates of relevance using ML and Neighbour-nets.
Newest work from us involving Ahmed Ali, @AG78617 and @Herr_Flow: we created a representation of the time-resolved photoswitching of PDZ3 by the Hamm group in MD simulations. Turns out: allostery here is a cooperative process, again! arxiv.org/abs/2209.07829
For everyone heading to the #DPG meeting in Regensburg and interested in microscopic sources of friction in biomolecules: @die_jaegerIn presents the results of our collaboration with @BalzerBizan and @HugelLab on directional friction tomorrow at 12 h in the session BP 15!
For all at the DPG meeting in Regensburg interested in machine learning on protein dynamics: visit the presentation of Daniel Nagel and @gegadiez on their developments of unsupervised and nearly parameter-free clustering methods for molecular features in session BP 15 at 11:45 h!
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Simon Bray @SimonBray18
114 Followers 227 Following Research software engineer at Gain Therapeutics, PhD student at the University of Freiburg. Working with virtual screening and scientific workflows.And that's a wrap for our RU-workshop "Reducing complexity of nonequilibrium systems"! A heartfelt thank you to all speakers and participants for making this meeting a success! And here some pictures of some serious efforts at barrier crossing and pathway sampling while hiking!
And that's (most likely) a wrap for the theoretical basis of our dissipation-corrected targeted MD (dcTMD) approach: we show how we can drive conformational transitions of a protein by simple pulling coordinates, 1/2 #compchem arxiv.org/abs/2309.08759
I am again grateful to @HugelLab and @BalzerBizan for the great collaboration - that was a really fun project!
Our article on anisotropic friction in @NanoLetters has made it to the Cover of the Journal! Props to @die_jaegerIn for the Cover art (I'm really happy that the introduction to Blender seminar I gave in the @MolDynFR group is bearing fruit)! pubs.acs.org/toc/nalefd/23/…
The Editors of @JCIM_JCTC (many thanks!) invited me to write a Perspective on "Predicting Protein–Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics" - here it finally is, I'm looking forward to your comments! pubs.acs.org/doi/10.1021/ac…
Many people have asked me how to pronounce my first name. To help out, I recorded its correct pronunciation using NameCoach. My first name is Xuhui, which means 'morning sunlight' in Chinese characters (旭辉). #MyNameIs name-coach.com/xuhuihuang
Finally out in @NanoLetters: Anisotropic Friction in a Ligand-Protein Complex. A great collaboration between W. Cai, @HugelLab and @BalzerBizan at @UniFreiburg, J. T. Bullerjahn at @MPIbp, while @die_jaegerIn and I did the MD simulations. #compchem pubs.acs.org/doi/10.1021/ac…
I saw the latest @Ducky3d tutorial and immediately thought, that I have to try this on a molecule (of course) 😁 I haven't done small molecules in a while, so that was fun! If you want to do so as well, the link is in a comment ⬇️ #sciart #Blender3d
New work by @_posti_ , @MolDynFR and me: theoretical framework how to analyse biomolecular pathways (here: of protein-ligand unbinding), calculate kinetics separately for paths and combine them into global rates. Out now in JCP as editors pick: #compchem aip.scitation.org/doi/10.1063/5.…
Last work of this year by @_posti_ , @MolDynFR and me: the physics of how (& why) to separate protein-ligand unbinding trajectories according to pathways, calculate rates per pathway & finally how to combine everything into a single rate. Preprint at arxiv.org/abs/2212.07154 .
Sacrificial bonds ✂️in collagen uncovered! Fantastic joint work of Benedikt with other @mattertolife students and wonderful collaboration with @grynova_CCC and David Hudson! Simulations 🤝experiments 🎉
"Collagen breaks at weak sacrificial bonds taming its mechanoradicals" biorxiv.org/content/10.110… We @graeter_mbm use our scale-bridging KIMMDY simulations to uncover molecular rupture sites in stressed collagen, which funnels ruptures into crosslinks taming the generated radicals.
The results of @SimonBray18 's Master thesis are (finally!!!) out with additional work from Victor Tänzel in @JCIM_JCTC : Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods #AI #machineLearnig #compchem pubs.acs.org/doi/10.1021/ac…
For everyone heading to the #DPG meeting in Regensburg and interested in microscopic sources of friction in biomolecules: @die_jaegerIn presents the results of our collaboration with @BalzerBizan and @HugelLab on directional friction tomorrow at 12 h in the session BP 15!
I can finally confirm: starting today, I have a permanent position at the University of Freiburg. I am beyond relief to finally being out of academias hamster's wheel, and incredibly grateful for all who supported me on the way, especially Gerhard Stock and all at @MolDynFR.
This was a fun project with a recall to time with bacteriorhodopsin: Nadja Helmer, @MolDynFR and I had a look at how 7TM photoproteins deal with excess energy after relaxation. Turns out: bR has a lightning rhod, while rhodopsin isn't good at dissipation. arxiv.org/abs/2208.10187
Newest work from Daniel Nagel and me at @MolDynFR finally published in @jctc_papers: Correlation-Based Feature Selection to Identify Functional Dynamics in Proteins doi.org/10.1021/acs.jc…: a 'divide and conquer' approach to separate the relevant dynamics of proteins from noise.
Newest work of us in @MolDynFR involving @_posti_ , @gegadiez and @BenjaminLickert out now in @JMolBiol as open access publication: Cooperative protein allosteric transition mediated by a fluctuating transmission network #biophysics #compchem #AI sciencedirect.com/science/articl…
dcTMD providing an insight into the "Molecular Origin of Driving-Dependent Friction in Fluids" - new work from us at @MolDynFR including @_posti_ now out in @jctc_papers ! #compchem pubs.acs.org/doi/10.1021/ac…
@Herr_Flow @MolDynFR @_posti_ @jctc_papers Fascinating work 😊
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