Philmus Lab

This is the lab account for the research lab of Dr. Benjamin (BJ) Philmus (he/him). College of Pharmacy at Oregon State and focusing on natural products.

[CHARMM-GUI @CharmmGui]

We have released three new modules: (1) Quick Bilayer, (2) Hybrid ML/MM Modeler, (3) Covalent Ligand Docker. Some video demos for (2) and (3) will be available this week.

[Vega Shah @dr_alphalyrae]

Introducing La-Proteina, a generative AI model that creates complete atomistic protein structures together with their amino acid sequences, scalable upto 800 residues. Built by @NVIDIA Research, in collaboration with @UniofOxford and @Mila_Quebec

La-Proteina addresses a key challenge in protein design by generating both backbone and side-chain atoms in a single unified process. It uses a hybrid architecture that models alpha-carbon coordinates while encoding sequence and side-chain details in latent vectors for every residue.

@DidiKieran @karsten_kreis @tomasgeffner @ArashVahdat

[Joint Genome Institute @jgi]

By investigating the role compounds produced by cyanobacteria gene clusters play in freshwater ecosystems, research by @PhilmusLab of @OSUPharmacy will support the development of predictive models of microbial behavior in terrestrial-aquatic interfaces.
https://t.co/4p3lQKASUr

[Indrek Kalvet @ikalvet]

RFdiffusion2 is now live!
https://t.co/H5bsYd0YuA

You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
Great job @r_krishna3 @woodyahern @dougtischer and everyone else!

[Gabe Nagy @g_nagy]

Our department is hiring! The Department of Chemistry at the University of Utah invites applicants for two tenure-track faculty positions at all ranks in the areas of 1) Biological Chemistry broadly defined and 2) Experimental Physical Chemistry.

https://t.co/gP7VCKDsUv

[Dr. Elizabeth Skellam @SkellamLab]

🚨We have a job opening to join our team! We're looking for a highly motivated and talented natural product chemist 👩‍🔬👨‍🔬🧪at the #postdoctoral level with experience isolating natural products from fungi 🍄and plants🪴using HPLC, MS/MS, and NMR techniques: https://t.co/ezcm2YeS3R

[Yudai Matsuda @ CityUHK @MatsudaLab]

Please RP🙏
We are still looking for faculty candidates in the areas of chemical biology, biological chemistry, or pharmaceutical sciences at @CityUChem. Join us in vibrant Hong Kong, a global hub for innovation and culture!　https://t.co/ZQy3vwqqEh

[Vega Shah @dr_alphalyrae]

For PhD students in my network, @nvidia is now accepting applications for our graduate fellowship program. If you are working on topics across AI, life sciences, healthcare and HPC - consider applying.
https://t.co/QW6MwNz9GQ

[Philmus Lab @PhilmusLab]

@joulesbrunelle Good gosh it has been a long time! She is going to do great things!

[bertbertbertlab @MattBertin2]

Please check out our lab's latest publication in Journal of Natural Products @pharmacognosy. It's a really fun story of chemical ecology and specialized chemistry. I'm grateful to Shiwei Chen and the other co-authors. https://t.co/9FlNcflfit

[Y. Katsu @ykguitar1002000]

Identification of a L‐threonine‐utilizing hydrazine synthetase for thrazarine biosynthesis in Streptomyces coerulescens MH802‐fF5 - Shikai - ChemBioChem - Wiley Online Library https://t.co/idqyuUYNLG

[Y. Katsu @ykguitar1002000]

Ketosynthase Domain Catalyzes β-Lactonization in the Biosynthesis of the HMG-CoA Synthase Inhibitor Hymeglusin | Journal of the American Chemical Society https://t.co/bAgB0JhDdV

[Shen Lab @lab_shen]

We’re hiring postdocs in the Shen Lab!

We're seeking candidates with expertise in:
🧪 Natural product discovery
🧬 Genome mining
⚗️ Synthetic chemistry & biocatalysis (esp. for ADCs)

Interested? Email Professor Shen with your CV + references:
🔗 https://t.co/fsgSxlUzJ4

[BT Murphy Lab @MurphyLabUIC]

Video: How the Big Beautiful Bill will degrade science, public safety, and the US economy.
https://t.co/XwIBRmo305

I made a video to show how NIH-university partnerships benefit society, and how Trump Administration policies have dismantled this essential pipeline.

[ShihLab @LabShih]

Check out our new preprint! We examined sources of variability of transgene expression in N. benthamiana agroinfiltration and ways to minimize it. Graduate student Sophia Tang observed FP expression in >1,800 plants over the course of nearly 3 years! https://t.co/dAYyhwrqRD

[Conor McClune @conor_mcclune]

Today in @Nature we report a systematic strategy to activate & identify gene sets in plants. We identify 8 new genes from the yew tree's Taxol biosynthetic pathway, enabling us to engineer tobacco with 17- & 20-gene pathways to Taxol precursors baccatin III and dBz-deoxy-Taxol. a thread 1/x..
https://t.co/9QdjOkqQQ1
With amazing coauthors @Sattely_lab @ctliu629 @fordycelab @Stanford_ChEMH @StanfordEng

[Philmus Lab @PhilmusLab]

@mkoeris Absolutely correct! @mkoeris How do us small labs get involed and help?

[Michael C. Jewett @MichaelCJewett]

Recombinant protein production remains more art than science. How can we "solve" the protein expression bottleneck? As proteins are involved in virtually every biotechnology process, this will transform the bioeconomy @erika_alden_d @Align_Bio

https://t.co/SXWteSX5gR

[Mark O. Martin @markowenmartin]

Looking for a microbial enthusiast to share their #MicrobialCentrism on my #MattersMicrobial podcast (https://t.co/57crtDRV5k) on June 26th between 7AM - noon. I have been writing to people but not a lot of traction yet. Please spread the word?
@asm.org
#TheMicrobesYoullKnow

[Marc Chevrette @wildtypeMC]

If you are a PhD student in microbial interactions or natural products that is displaced by this political bullshit and looking for a new lab, I have room for one (or potentially two) PhD students in my group in the fall when I move to UW. Feel free to reach out via email.