Bercem Dutagaci

Faculty at the University or California Merced - Computational Biophysics/Biology

[Bercem Dutagaci @BDutagaci]

We are hiring a postdoctoral scholar @ucmerced to work on an NIH-funded project studying transcription using #MDsimulations and #MachineLearning: https://t.co/kYg49OAXuK. Please spread the word!

[Bercem Dutagaci @BDutagaci]

Our paper on the Pol II-DSIF complex is now published in JCIM. We showed that DSIF alters the dynamics of nucleic acids and the Pol II and allosterically impacts the active site. @ACSPublications @JCIM_JCTC https://t.co/yVRge3tZgL

[Bercem Dutagaci @BDutagaci]

Our new preprint on the RNA polymerase-DSIF complex is now online on @biorxivpreprint . MD simulations showed how DSIF altered the dynamics of Pol II and nucleic acids and suggested an allosteric impact on the active site.

[bioRxiv Biophysics @biorxiv_biophys]

Molecular Basis for Impacts of DSIF on the Dynamics of RNA Polymerase II Elongation Complex https://t.co/7UhGTx7xZ1 #biorxiv_biophys

[The Journal of Physical Chemistry @JPhysChem]

This computational study from @bdutagaci Lab shows how hydrophobic interactions, H-bonding, and ion-mediated electrostatic interactions play roles in the clustering of RNA polymerase CTD.
https://t.co/JV16TXIhfo

[Bercem Dutagaci @BDutagaci]

@alex_mackerell Thank you, Alex!

[Bercem Dutagaci @BDutagaci]

Our new work on CTD of RNA Pol II is now available on @JPhysChem. We showed how crowding and phosphorylation play roles in the conformations and clustering of CTD models at atomistic details. https://t.co/7W8cTCVPAM

[Bercem Dutagaci @BDutagaci]

Our new preprint on RNA polymerase CTD is now online @biorxivpreprint @biorxiv_biophys: https://t.co/keutZmdkQ4 Our simulations suggest that phosphorylated CTD models form clusters via hydrogen bonding and counter-ion-mediated electrostatic interactions.

[Alberto Perez @Al__Perez]

we are looking for a #compchem postdoc to work on an NIH funded project to characterize BET proteins, the complexes it forms, and identifying new viral and host PPIs. Someone with expertise in MD, python, ML, and a passion to solve biological puzzles is a great fit! Pls RT

[Shahar Sukenik @shaharsu]

Come work with us!! We're developing exciting new quantitative methods to reveal how biology survives in extreme dehydration 🏜️. DMs open if you're interested.

[Bercem Dutagaci @BDutagaci]

@Vikasku94778753 @ucmerced Thank you!

[Bercem Dutagaci @BDutagaci]

Our work @ucmerced is published in the Journal of Computer-Aided Molecular Design. We showed how small molecules, which inhibit mutant huntingtin gene transcription, affect the dynamics of the Pol II-DSIF complex. https://t.co/aYhLOoF4RX

[The Journal of Physical Chemistry @JPhysChem]

Using MD simulations, @bdutagaci and Weththasinghage Amith from @ucmerced obtained conformational spaces of Pol II CTD models and showed how the phosphorylation pattern and length of CTD models have complex effects on the conformations
https://t.co/ksGWyqL3EA

[Bercem Dutagaci @BDutagaci]

Our paper on RNA polymerase II CTD is now available on @JPhysChem. We showed how the conformational spaces of CTD depend on the length and phosphorylation pattern. https://t.co/HFSkz3QARV

[Bercem Dutagaci @BDutagaci]

Our preprint about RNA polymerase II CTD is now available on @biorxivpreprint. We learned that CTD shows complex structural behaviors upon phosphorylation. https://t.co/iBiph8Ia27

[bioRxiv Biophysics @biorxiv_biophys]

Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 A using a free-electron laser https://t.co/qGpDpn7kZT #biorxiv_biophys

[Bercem Dutagaci @BDutagaci]

Our preprint on small molecule inhibition of Spt5 function is now available online! We predicted the binding sites of the molecules and their effects on the dynamics of the Pol II elongation complex.

[bioRxiv Biophysics @biorxiv_biophys]

Binding of Small Molecule Inhibitors to RNA Polymerase-Spt5 Complex Impacts RNA and DNA Stability https://t.co/DgPjKxCUhd #biorxiv_biophys

[Chris Amemiya @chris_amemiya]

Postdoc position in a lab doing really innovative and interdisciplinary work.

[Bercem Dutagaci @BDutagaci]

Our preprint about RNA polymerase II CTD is now available on @biorxivpreprint. We learned that CTD shows complex structural behaviors upon phosphorylation. https://t.co/iBiph8Ia27

[Bercem Dutagaci @BDutagaci]

Our work on Pol II TL mutations is now published in @PLOSCompBiol We characterized functional phenotypes and their structural outcomes using MD and ML. https://t.co/WHJc0cws2X

[Ute Hellmich @HellmichGroup]

Do a PhD with us in beautiful Jena! Structural dynamics of the membrane machines microbes use to talk to each other & sense their🌍!
info: https://t.co/BTzCtfolhm

Collab with @OConnor_lab within @MPI_CE IMPRS, @microverse_exc & @JSMC_Info!
#TCS #IntegratedStructuralBiology

[peter walhout @PWalhout]

I am thrilled that this massive paper is finally published! Fully atomistic molecular dynamics simulations of small molecule diffusion in dilute polyelectrolyte systems.
https://t.co/5zHZcaq19H