Lightnews — Scholar-powered news

Rafael Najmanovich @rnajmanovich.bsky.social · Mar 24

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

Gonzalo Parra @gonzaparra.bsky.social · Mar 22

Everything comes to an end but memories remain!!
We had a great 3DSIG/3DBioinfo event in "sunny" Barcelona this week!! I have enjoyed so much to help organising it & to have such great minds all together sharing science for 3 days!!

Aufwiedersehen friends! For more science & friendships to come! ⭐

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Reposted by Rafael Najmanovich

chelsea g. summers @chelseagsummers.bsky.social · Mar 19

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...

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...

www.lemonde.fr

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Rafael Najmanovich @rnajmanovich.bsky.social · Mar 9

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.

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Rafael Najmanovich @rnajmanovich.bsky.social · Mar 8

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.

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Rafael Najmanovich @rnajmanovich.bsky.social · Feb 22

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.

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Feb 22

NRGRank: Coarse-grained structurally-informed ultra-massive virtual screening https://www.biorxiv.org/content/10.1101/2025.02.17.638675v1

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Rafael Najmanovich @rnajmanovich.bsky.social · Feb 10

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

Peter Škrinjar @peterskrinjar.bsky.social · Feb 8

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!

www.biorxiv.org/content/10.1...

🧵👇 (1/n)

Have protein-ligand co-folding methods moved beyond memorisation?

Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...

www.biorxiv.org

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Reposted by Rafael Najmanovich

Florian Jug @florianjug.bsky.social · Jan 29

🚨🚨 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

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Reposted by Rafael Najmanovich

Doug Kojetin @dougkojetin.bsky.social · Jan 24

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

Derek Lowe @dereklowe.bsky.social · Jan 24

This one is mostly about the title subject (featuring a very interesting compound from academia) but it’s also about attacking the NIH:

Attacking Estrogen-Receptor-Positive Breast Cancer

www.science.org

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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 ...

doi.org

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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 ...

doi.org

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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 ...

doi.org

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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 ...

doi.org

1

Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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 ...

doi.org

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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)

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 ...

doi.org

1

Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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

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Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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

Rafael Najmanovich @rnajmanovich.bsky.social · Jan 24

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.

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Jan 24

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 https://www.biorxiv.org/content/10.1101/2025.01.23.634566v1

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 19

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.

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 19

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?

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 19

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.

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,...

www.biorxiv.org

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Reposted by Rafael Najmanovich

eLife @elife.bsky.social · Dec 10

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.

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…

buff.ly

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 10

(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.

Rafael Najmanovich @rnajmanovich.bsky.social · Dec 10

(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.

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 10

(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.

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Rafael Najmanovich @rnajmanovich.bsky.social · Dec 10

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

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