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Learning new skills at Sponer lab

Our work presented at the 16th Christmas Biophysics Workshop in Brdo xbw2022.ijs.si/index.html Valerio Piomponi will present our work on integrating experiments and molecular simulations to model the dynamics of modified #RNA

Our work presented at the EutopiaCOST workshop Structure and Topology of #RNA in living systems in Trento! Valerio Piomponi will talk today about how we combine #moleculardynamics simulations and experimental data to describe the dynamics of modified nucleotides indico.ectstar.eu/event/185/prog…

I’m excited to share that our work of alchemical metadynamics has been published in JCTC Papers JCIM & JCTC Journals ! Thanks to Michael Shirts for his guidance along the way and I also appreciate the substantial input from Valerio Piomponi and Giovanni Bussi ! pubs.acs.org/doi/10.1021/ac…

Our work presented today at the Chemistry department stc.uniroma2.it Università di Roma Tor Vergata! Giovanni Bussi will show #RNA dynamics from integrating #MD simulations, #SAXS, #NMR, and #SHAPE, as done by Mattia Bernetti Valerio Piomponi and Nicola Calonaci. Thanks Paolo Calligari for the invitation!

Our work presented this week at #EBSA2023 session ‘Biophysics of #RNA and ribosomes’ on Wed morning at 8:30, room B. Valerio Piomponi will show how we use #MD, #NMR, and #SAXS to reconstruct the dynamics of A-to-I edited dsRNA. Collab with @Sattler_lab

Glad to had the opportunity to present part of my PhD work at the"Biophysics of RNA and ribosome" session of #EBSA2023. bussilab

3 days left to apply for a PhD position in Physics and Chemistry of Biological Systems SBP Sissa SISSA . Application and entrance exam are online. More info 👇Please RT, and apply!

Postdoc available in my lab starting Dec 2023 on classical and QM/MM MD simulations to refine structures and assign metal ions within cryo-EM maps of RNA molecules. For info or to apply send me a cover letter & CV! Project in collaboration with bussilab and experimentalists.

Excited to share our new #preprint on #m6A's role in #RNA recognition! 🧬 A collaborative effort by Valerio Piomponi, Miroslav Krepl, Sponer lab, & Giovanni Bussi. Dive into our findings in this thread 👇

#prpconference2024 on pandemic preparedness: meet the speakers! We are pleased to introduce Tulio de Oliveira who will give a talk on "Using genomics to understand climate amplified diseases and epidemics”. To learn more on the International Conference: bit.ly/3x6HcIt

It was a great pleasure to deliver a LADE seminar at Area Science Park in #Trieste! Big thanks to Francesca Cuturello and Alessio Ansuini alessio ansuini for having me here! scientific-events.areasciencepark.it/event/raffaell…

📢 Our work on #m6A role in #RNA recognition has been published on The Journal of Physical Chemistry B! doi.org/10.1021/acs.jp… An effort led by Valerio Piomponi with help from Miroslav Krepl, Sponer lab, and Giovanni Bussi Summary in the cited post 👇

.Valerio Piomponi, Miroslav Krepl, Sponer lab, & Giovanni Bussi investigate the role of #m6A in #RNA recognition! #metadynamics, replica exchange, and alchemical calculations combined to sample RNA:YTH complex conformations, focusing on hydration dynamics. go.acs.org/aQD

Il nuovo studio del laboratorio di Data Engineering utilizza l'#AI per prevedere l'impatto delle mutazioni genetiche sulla stabilità delle proteine, aprendo la strada a innovazioni nella ricerca biomedica >> bit.ly/3Y5IXj9

New dataset (DPCfam-UHGP50) developed by LADE - Data Engineering Laboratory to improve protein sequence annotation and promote discoveries in metagenomics: a valuable resource for a better understanding of the human gastrointestinal proteome. More info: bit.ly/4eYFR7X

Can we predict, at very early stages of a viral outbreak, potential mutations in viral proteins, which might emerge in viral variants? Martin Weigt’s speech opens the second session of the day at #prpconference2024

MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data • MDRefine is a novel Python package that refines molecular dynamics (MD) simulation trajectories by integrating experimental data, improving alignment with observed molecular

Just started my migration to🦋, I hope to see all of you there very soon!

Evolutionary constraints guide AlphaFold2 prediction of alternative conformations and inform rational mutation design 1. This study introduces a refined method to guide AlphaFold2 toward predicting alternative protein conformations by clustering homologous sequences using MSA