Manuel N. Melo at ITQB NOVA

ITQB NOVA (Universidade Nova de Lisboa), EvaMobs’ coordinator, will host European RosettaCon 2026!

Theme: “Crossing Boundaries with Protein Design”
📅 28–30 Oct 2026 | 📍 Lisbon

Registration & abstracts open in March.
Details: europeanrosettacon.org

#RosettaCon #ProteinDesign @itqbnova.bsky.social

Shout out to @marmakow.bsky.social for getting our work on AMP-lipid interplay featured as JCIM's cover for the May 12 issue! 🎉
pubs.acs.org/doi/10.1021/...

And a big thanks to @tempo3dstudio.bsky.social for the great illustration 🖌️

#compchem #compbiophys #compbiol

Martini workshop registration now open !!!!
See cgmartini.nl for details and how to apply.
Looking forward to seeing you in Groningen, Aug 11-15th.

GitHub - MeloLab/GangliosideParameters: Martini 3 parameters for GM1 and GM2 Martini 3 parameters for GM1 and GM2. Contribute to MeloLab/GangliosideParameters development by creating an account on GitHub.

To all Martini 3 ganglioside lovers: here's an open-beta set of parameters for GM1 and GM2 from yours truly and @martitoti.bsky.social.
Enjoy!

github.com/MeloLab/Gang...

Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide An intriguing feature of many bacterial membranes is their prevalence of non-bilayer-forming lipids, such as the cone-shaped phosphatidylethanolamines and cardiolipins. Many membrane-active antimicrob...

Cool new AMP pore structures and a membrane activity dependent on lipid shape, in our new paper by @marmakow.bsky.social!
(Using the old-but-gold Martini 2 model from @cg-martini.bsky.social)
#compchem #compbiophys #compbiol 🖥️🧪

pubs.acs.org/doi/full/10....

More VDAC shenanigans, now in interaction with Hexokinase I, in another great collaborative work with @holthuislab.bsky.social and @cg-martini.bsky.social!

www.nature.com/articles/s42...

It was great to be part of this enormous effort spanning several years.

Big cheers to the Martini 3 Lipid Taskforce crew, especially Kasper and @pauloctsouza.bsky.social!

#compchem #moleculardynamics

Martini 3 coarse-grained models for carbon nanomaterials The Martini model is a coarse-grained force field allowing simulations of biomolecular systems as well as a range of materials, including different types of nanomaterials of technological interest. Re...

Martini 3 parameters for carbon nanomaterials, including my nanotubes.
#CompChem
chemrxiv.org/engage/chemr...

Check out the cool work by our colleagues at the @itqbnova.bsky.social Cordeiro Lab!

Cloud of words in various colors and sizes. Some of the largest words include peptide membrane model protein simulation interaction molecular cell lipid fusion antimicrobial dynamics martini results activity bp100 coarsegrained binding can mechanism.

Yup, this tracks.
Thanks scholargoggler.com 💬☁️

👋
The Melo lab checking in from Portugal!

Excited to share that our recent research using #Martini3 #CG simulations on the role of Spc2 in the yeast signal peptidase complex (SPC) has been published in the Journal of Cell Biology.

Read the full article here: rupress.org/jcb/article/...

Great initiative! Could you add me? Thanks!

GitHub - MeloLab/CofactorParameterization: Nucleotide cofactor parameters developed for Martini 2.2 and 3. Nucleotide cofactor parameters developed for Martini 2.2 and 3. - MeloLab/CofactorParameterization

In need of some Martini 3 CG parameters for stuff like ATP, NAD+/NADH or FAD?

We just made parameters for those and several other molecules public while the preprint is in the works!

Check out the lab's repository at github.com/MeloLab/Cofa... 🖥️🧑‍🔬

We're now on Bluesky! (@melolab.bsky.social)
Hope you all join soon!

Great to be a part of this effort!
Congrats, @SilvaPereiraLab! https://twitter.com/itqbnova/status/1747948949023969598

And our new Martini 3 cholesterol model is out!
https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00547

Big shout out to @SouzaPauloCT and all the collaborators behind this huge effort!

We just opened registrations and abstract submissions for the XVIII Iberian Peptide Meeting later this fall. Be sure to check the meeting's website for more info https://iberian-peptide-meeting.github.io/XVIII/ See you in Sesimbra!

Martini 3 Coarse-Grained Force Field for cholesterol Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and the inclusion of new bead types and sizes. However, the release of the new model resulted in the need to re-parameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving overall behavior.

And after the GitHub soft opening, here's the preprint for our Martini 3 cholesterol parameterization!
https://chemrxiv.org/engage/chemrxiv/article-details/64677ce5fb40f6b3eed8bb26

Big cheers, @SouzaPauloCT, @CG_Martini and the many others in this amazing collaborative endeavor!

Karl and Fernando's work on some Martini 3 wrinkles just became full article!
https://t.co/fD0fS2ujay

Also, since last tweet, the lab has
i) been at the Martini dev meeting in Malta 😍🍸

ii) organized the 2022 @3dBioinfoPT actions 💪
https://t.co/zguVyJQ7MN

Exciting semester!

Frontiers | SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is havi...

Congrats @MaryVallerio and Luís Borges-Araújo for the publication of our analysis of the SARS-CoV-2 RBD dynamics, and how it may explain some of the variants' success.

Check it out 😃
https://www.frontiersin.org/articles/10.3389/fmedt.2022.1009451

Check out our preprint on some Martini 3 rough edges when modeling helical peptides in specifc dimeric or transmembrane conditions. Keeping it challenging for upcoming refinements to the force field by @CG_Martini, @SouzaPauloCT and us! https://doi.org/10.26434/chemrxiv-2022-wgz1j

Registration is open for the 3D-BioInfo-PT Introductory Workshop, Sept. 22-23 2022 at ITQB NOVA! Come get your feet wet in the field of structural computational biology. Organized by your truly and with support of @BioData_pt and @itqbunl. Enroll at https://t.co/UXDUyiJKbW

Portugueses descobrem a estrutura porosa que abre a porta à bronquiolite e pneumonia Uma equipa portuguesa descobriu o mecanismo que permite aos vírus parainfluenza infectar as células humanas, através da criação de uma estrutura até agora desconhecida. Esta estrutura permite a fusão do vírus com a membrana das nossas células.

And the news already made it to non-academic media 😀
Extra outreach points, @MaryVallerio!
https://www.publico.pt/2022/07/26/ciencia/noticia/portugueses-descobrem-estrutura-porosa-abre-porta-bronquiolite-pneumonia-2014503

Great job, @MaryVallerio, on getting our paper's art on the ACS Chem Biol front cover! Check out the multidisciplinary work, with a dash of @SouzaPauloCT and @CG_Martini's Martini 3, at https://pubs.acs.org/doi/10.1021/acschembio.2c00208 #MyACSCover #compchem

Calls are open for the @FundlaCaixa INPhINIT doctoral fellowships!
Interested in a PhD in sunny Lisbon with top players in the field? Then check out our suberin modeling project, with a dash of experimental validation, co-hosted with the @SilvaPereiraLab!
https://t.co/NdQcbHtfVw

Coimbra will be the place to be, on the 21 and 22 of December, to hone your CompBiol skills.
And the @MeloLab will be lecturing, to cater to all your Martini coarse-graining needs! https://twitter.com/BioDataPT/status/1450817222247698434

Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse Grain Force Field Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of molecular dynamics simulation studies of biological membranes, in particular of those employing coarse-grain models because of the potential long times and sizes of the involved membrane processes. Version 3 of the widely used Martini coarse grain force field has been recently published, greatly refining many aspects of biomolecular interactions. In order to properly use it for lipid membrane simulations with phosphoinositides, we put forth the Martini 3-specific parameterization of inositol, phosphatidylinositol, the seven physiologically relevant phosphorylated derivatives of phosphatidylinositol. Compared to parameterizations for earlier Martini versions, focus was put on a more accurate reproduction of the behavior seen in both atomistic simulations and experimental studies, including the signaling relevant phosphoinositide interaction with divalent cations. The models we develop improve upon the conformational dynamics of phosphoinositides in the Martini force field and provide stable topologies at typical Martini timesteps. They are able to reproduce experimentally known protein-binding poses as well as phosphoinositide aggregation tendencies. The latter were tested both in the presence and absence of calcium, and include correct behavior of PI(4,5)P2 calcium-induced clusters, which can be of relevance for regulation.

Our shiny new CG parametrization of phosphoinositides, upgraded for @CG_Martini's Martini 3, is just out as a ChemRxiv preprint. Enjoy!

https://t.co/uygbmTznih

Be sure to check the goods at our development GitHub repo: https://t.co/hPWaxE7Cgp

Our newest work on @CG_Martini parameterization is out, for all your CG nucleotide cofactor needs!

Congrats to @ms_flip for his effort combining computation with experiment, essential to pulling this off.

https://pubs.acs.org/doi/10.1021/acs.jcim.0c01077