Rafael Najmanovich

It was a great meeting. Thank you @gonzaparra.bsky.social for making sure every detail worked out - except for the rain... :)

Etats-Unis : un chercheur français refoulé pour avoir exprimé « une opinion personnelle sur la politique menée par l’administration Trump » Le ministre de la recherche français a dit sa « préoccupation », mercredi, après cette décision des autorités américaines. Le chercheur du CNRS aurait subi un contrôle aléatoire à son arrivée, avant q...

So on March 9, a French scientist, on a visa to attend a conference in Houston, was denied entry to the US and subsequently expelled because his phone had messages decrying scientific policies put forward by the Trump administration: www.lemonde.fr/internationa...

NRGRank, with which you can screen 10^6 molecules per day in a modern laptop, is out. Particularly useful for apo form or AlphaFold models but in all cases (including hole), finding binders that are missed by Glide (the opposite is also true). NRGRank requires 0.3s/compound - 100-1000 fold faster.

was going to send you a DM as I prefer not to discuss politics in public but found out your profile does not allow DMs.

Happy to share our latest preprint. With NRGRank you can screen 1M in a day in a laptop (use our NEGSuite-Qt for that) - a billion compounds per day with our computational resources.

"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."

🚨🚨 MEGA JOB ALERT 🚨🚨
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!

Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏

More details below... check it out! 🧵 1/3

In The Pipeline blog featuring estrogen receptor papers with contributions from @nrimpact.bsky.social members @docfanning.bsky.social and @nelsonlab.bsky.social #nuclearreceptors

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

IsoMIF for the detection of binding-site similarities with applications in drug repurposing, and to corroborate screening/docking results for molecules with known targets. Lastly, if you obtain a Modeller license, it allows you to perform mutations within PyMOL. Check it out.

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

NRGTEN to generate conformational ensembles, to predict the effect of mutations on protein flexibility and stability, to generate dynamical signatures for mutants (say you want to increase stability without affecting binding-site flexibility);

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

FlexAID for docking simulations and to refine approximate poses obtained with NRGRank; Surfaces to analyse protein-ligand and protein-protein interfaces with accuracy equivalent to MD-based FEP calculations in predicting DDG of mutations;

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

The tools are: GetCleft for the definition and refinement of cavities; NRGRank for ultra-massive virtual screening (50K molecules/h in a laptop), pre-loaded molecule datasets (all FDA approved drugs, all ligands in PDB, all tetra peptides);

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

Their combination in this plugin makes it possible to perform complex and innovative workflows in understanding protein function, drug development and protein engineering. (2/N)

NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities We introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the ...

I am following up on the previous post with a little more detail. The NRGSute-Qt is a PyMOL plugin to use our major computational tools. Tools that offer high-performance, speed and ease of use. (1/N)

I don'y like mate but I like this paper, what a monumental achievement, from genome to structure/function. Wow.

let alone that any health intervention may take upwards of 15 years alone to be approved...

Our newest preprint is out. A PyMOL plugin giving access to a broad suite of high-performance, fast, and easy to use methods for virtual screening (50K molecules/h), docking, analysis of molecular interactions, dynamics, engineering permitting complex workflows.

It is happening to our preprint too, It is a new outreach program to expand the visibility of research - people interested in our research get to hear about someone else's upon reading what was supposed to be our abstract... and someone else is reading our abstracts elsewhere too.

Thanks Nathanael - we need to catch up - I am aware I let the ball drop on that email you sent me long ago. Can we do a zoom in the new year?

Comprehensive Analysis of SARS-CoV-2 Spike Evolution: Epitope Classification and Immune Escape Prediction The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprece-dented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,...

Anyone else experiencing problems with @biorxivpreprint.bsky.social ? Like preprints with mismatched abstracts? it is happening to my latest: www.biorxiv.org/content/10.1... - although when originally published it was all fine.

Changes to eLife’s indexing status in Web of Science and Scopus To best serve the needs of researchers, eLife will provide a partial feed of research to be indexed in the Web of Science Core Collection. eLife will also move from the Scopus Journals Collection to…

After listening to community feedback, we will provide a partial feed allowing 93% of eLife authors to continue being indexed in the Web of Science Core Collection. We will also move from the Scopus Journals Collection to the Scopus Preprints Collection.

Full update below.

(5/5) We characterize the patterns of glycosylation and its role in mediating Ab binding and conformational stability. This study was performed entirely with experimental structures, 1560 in total and without the incredible efforts of the structural community it would not have been possible.

(4/N) Enthalpic trade-off mutations in the RBM favour immune escape at the expense of ACE2 binding, whereas entropic trade-off mutations do not affect RBM but favour the closed state, thus entropically decreasing ACE2 binding.

(3/N) We perform a longitudinal analysis of the effect of mutations, we show the changing epistatic effect of mutations, define two evolutionary trade-off hypotheses for viral evolution: Enthalpic and Entropic.

(2/N) We use a combination of Surfaces' energies and geometry to define 14 epitope classes that go beyond Barnes' classes

(1/N) In this latest preprint, we employ our Surfaces method (Teruel, 2023) to predict
@jbloomlab.bsky.social
immune escape with excellent Pearson's r correlations.

Comprehensive Analysis of SARS-CoV-2 Spike Evolution: Epitope Classification and Immune Escape Prediction The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprecedented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,560 published Spike protein structures, capturing most variants that emerged throughout the pandemic and covering diverse heteromerization and interacting complexes. We employ an interaction-energy informed geometric clustering to identify 14 epitopes characterized by their conformational specificity, shared interface with ACE2 binding, and glycosylation patterns. Our per-residue interaction evaluations accurately predict each residue's role in antibody recognition and as well as experimental measurements of immune escape, showing strong correlations with DMS data, thus making it possible to predict the behaviour of future variants. We integrate the structural analysis with a longitudinal analysis of nearly 3 million viral sequences. This broad-ranging structural and longitudinal analysis provides insight into the effect of specific mutations on the energetics of interactions and dynamics of the SARS-CoV-2 Spike protein during the course of the pandemic. Specifically, with the emergence of widespread immunity, we observe an enthalpic trade-off in which mutations in the receptor binding motif (RBM) that promote immune escape also weaken the interaction with ACE2. Additionally, we also observe a second mechanism, that we call entropic trade-off, in which mutations outside of the RBM contribute to decrease the occupancy of the open state of SARS-CoV-2 Spike, thus also contributing to immune escape at the expense of ACE2 binding but without changes on the ACE2 binding interface. This work not only highlights the role of mutations across SARS-CoV-2 Spike variants but also reveals the complex interplay of evolutionary forces shaping the evolution of the SARS-CoV-2 Spike protein over the course of the pandemic. ### Competing Interest Statement The authors have declared no competing interest.

and also our latest work, Natálias latest preprint, a collaboration with the groups of
@mattbashton.bsky.social and Ricardo Rajsbaum is out in BioRxiv. www.biorxiv.org/content/10.1...

Congratulations to Dr. Natalia Teruel, who successfully defended her PhD yesterday, her work was judged to be exceptional and worth to be added to the Faculté de médecine - Université de Montréal rector's honours list.

Lets make our very own!

Why Do We Dream? A New Theory on How It Protects Our Brains "Dreams are primarily visual precisely because this is the only sense that is disadvantaged by darkness."

Fascinating theory of why we dream. time.com/5925206/why-...