Greg Bowman

Greg Bowman

@drgregbowman.bsky.social

Scientist. Christ-follower. Prof @UPenn. Director of Folding@home. Legaly blind. Father.

1.8K followers276 following98 posts

Greg Bowman reposted

Cecilia Clementi
@cecclementi.bsky.social

Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415... I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.

doi.orgNavigating protein landscapes with a machine-learned transferable coarse-grained model - Nature ChemistryThe development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...

Greg Bowman reposted

Frank Noe
@franknoe.bsky.social

BioEmu now published in @science.org !! What is BioEmu? Check out this video: youtu.be/LStKhWcL0VE?...

science.orgScalable emulation of protein equilibrium ensembles with generative deep learningFollowing the sequence and structure revolutions, predicting functionally relevant protein structure changes at scale remains an outstanding challenge. We introduce BioEmu, a deep learning system that...
Microsoft Research@msftresearch.bsky.social

Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...

Greg Bowman reposted

Xuhui Huang
@xuhuihuangchem.bsky.social

Excited to share our latest paper on @natcomputsci.nature.com‬! We present MEMnets, a deep learning framework for coarse-graining protein dynamics, driven by an analytical statistical mechanics theory to minimize memory kernels. Congratulations to all the authors! @uwmadisonchem.bsky.social

Nature Computational Science@natcomputsci.nature.com

📢 @xuhuihuangchem.bsky.social and colleagues present MEMnets, combining statistical mechanics theory with DL to find the slowest collective variables for biomolecular dynamics. @uwdsi.bsky.social @uwmadscience.bsky.social #chemsky www.nature.com/articles/s43... 🔓https://rdcu.be/eqnCf

nature.comMemory kernel minimization-based neural networks for discovering slow collective variables of biomolecular dynamics - Nature Computational ScienceThis study presents MEMnets, an approach that integrates statistical mechanics with deep learning to identify the slowest collective variables for biomolecular dynamics. MEMnets effectively captures m...

Greg Bowman reposted

Caroline Lynn Kamerlin ☀️
@lynnkamerlin.bsky.social

Our latest paper "Enzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic Hotspots" now out in JACS @jacs.acspublications.org. Collaboration with Jose M. Sanchez-Ruiz in Granada, among others. pubs.acs.org/doi/full/10....

pubs.acs.orgEnzyme Enhancement Through Computational Stability Design Targeting NMR-Determined Catalytic HotspotsEnzymes are the quintessential green catalysts, but realizing their full potential for biotechnology typically requires improvement of their biomolecular properties. Catalysis enhancement, however, is often accompanied by impaired stability. Here, we show how the interplay between activity and stability in enzyme optimization can be efficiently addressed by coupling two recently proposed methodologies for guiding directed evolution. We first identify catalytic hotspots from chemical shift perturbations induced by transition-state-analogue binding and then use computational/phylogenetic design (FuncLib) to predict stabilizing combinations of mutations at sets of such hotspots. We test this approach on a previously designed de novo Kemp eliminase, which is already highly optimized in terms of both activity and stability. Most tested variants displayed substantially increased denaturation temperatures and purification yields. Notably, our most efficient engineered variant shows a ∼3-fold enhancement in activity (kcat ∼ 1700 s–1, kcat/KM ∼ 4.3 × 105 M–1 s–1) from an already heavily optimized starting variant, resulting in the most proficient proton-abstraction Kemp eliminase designed to date, with a catalytic efficiency on a par with naturally occurring enzymes. Molecular simulations pinpoint the origin of this catalytic enhancement as being due to the progressive elimination of a catalytically inefficient substrate conformation that is present in the original design. Remarkably, interaction network analysis identifies a significant fraction of catalytic hotspots, thus providing a computational tool which we show to be useful even for natural-enzyme engineering. Overall, our work showcases the power of dynamically guided enzyme engineering as a design principle for obtaining novel biocatalysts with tailored physicochemical properties, toward even anthropogenic reactions.

Greg Bowman reposted

Richard Sever
@richardsever.bsky.social

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

openrxiv.orgHomepage - openRxivopenRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

Greg Bowman reposted

Sukrit Singh
@sukritsingh92.bsky.social

This work is now published in J Phys Chem B! Check out our work showing that simulations predict the impact of distal mutations on kinase-inhibitor binding, and our experimental NanoBRET dataset of 94 kinase mutations that provide a benchmark for future methods. Link: pubs.acs.org/doi/full/10....

Sukrit Singh@sukritsingh92.bsky.social

New preprint! We prospectively evaluate structure-based methods and measure how well they classify clinical kinase mutations as inhibitor–resistant or –sensitizing when compared against our NanoBRET assay. Alchemical methods are well-suited to modeling distal mutants! Link: doi.org/10.1101/2024...

doi.orgProspective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor bindingSmall molecule kinase inhibitors are critical in the modern treatment of cancers, evidenced by the existence of over 80 FDA-approved small-molecule kinase inhibitors. Unfortunately, intrinsic or acqui...

Greg Bowman reposted

Jonathan Wosen
@jonathanwosen.bsky.social

Breaking news: A judge has issued a national preliminary injunction blocking Trump cuts to NIH research overhead payments, a decision that suggests plaintiffs seeking to overturn the policy change are likely to eventually succeed. My latest for @statnews.com www.statnews.com/2025/03/05/n...

statnews.comJudge issues preliminary injunction blocking Trump cuts to NIH research overhead paymentsA federal judge issued a nationwide preliminary injunction blocking the Trump administration from slashing NIH payments for research overhead

Greg Bowman reposted

Samuel Sledzieski
@samsl.io

Seq2Symm is out now in @naturecomms.bsky.social! PLMs continue to be unreasonably efficient-- even for highly divergent sequences. Meghana and Minkyung did a great job leading on this! 📄: www.nature.com/articles/s41... 💻: github.com/microsoft/se...

nature.comRapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm - Nature CommunicationsSeq2Symm is a sequence-based AI model designed to predict the symmetry of protein structures composed of identical chains, known as homo-oligomers. It surpasses existing methods in accuracy and effici...

Greg Bowman reposted

Xuhui Huang
@xuhuihuangchem.bsky.social

Our perspective on using computational tools to design bacterial RNA polymerase inhibitors is out in the "Computational Biochemistry" special issue of ACS Biochemistry. Congratulations to Eshani! pubs.acs.org/doi/full/10....

pubs.acs.orgTargeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant PathogensThe increase in antimicrobial resistance presents a major challenge in treating bacterial infections, underscoring the need for innovative drug discovery approaches and novel inhibitors. Bacterial RNA...

Greg Bowman reposted

Gabriela K Popescu
@popstarlab.bsky.social

Guidance given to hostages can foster psychological flexibility in tough times. ▪︎ Choose your attitude and actions, even in difficult circumstances. ▪︎ Maintain self-discipline and mental stimulation so you are ready for the next step. ▪︎Plan for a better future to maintain hope.

psychologytoday.comIn Tumultuous Times, Think Like a HostageFeeling like a hostage? Learn psychological strategies from POWs and hostages to maintain resilience, resist despair, and plan for a brighter future in these turbulent times.

Greg Bowman reposted

Frank Noe
@franknoe.bsky.social

Today we have published BioEmu-Benchmarks (MIT license): a code to evaluate the multi-conformation sampling benchmarks, MD free energy landscape benchmarks, and folding free energy benchmarks shown in the BioEmu-1 paper with BioEmu or your own model. Some details below 🧵 github.com/microsoft/bi...

github.comGitHub - microsoft/bioemu-benchmarks: Benchmarking code accompanying the release of `bioemu`Benchmarking code accompanying the release of `bioemu` - microsoft/bioemu-benchmarks

Greg Bowman reposted

Greg Bowman
@drgregbowman.bsky.social

Three talks from my group on Sunday at #BPS2025 Cryptic pockets in crowded environments 9:30am in Rm 502A Allosteric glues inhibit G proteins noon in Rm 515B Antibody dynamics 5:30pm in Rm 502A

Greg Bowman reposted

Stand Up for Science!
@standupforscience.net

Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence

Greg Bowman
@drgregbowman.bsky.social

Three talks from my group on Sunday at #BPS2025 Cryptic pockets in crowded environments 9:30am in Rm 502A Allosteric glues inhibit G proteins noon in Rm 515B Antibody dynamics 5:30pm in Rm 502A

Greg Bowman reposted

Mark Cuban
@mcuban.bsky.social

This is the most relevant article to NIH and research cuts I’ve seen. Imagine if this was today , how many people would be saying “Why are we studying Gila Monsters and their impact on diabetes ? That’s wasted money !” globalnews.ca/news/9793403...

globalnews.caHow a Canadian scientist and a venomous lizard helped pave the way for Ozempic - National | Globalnews.caIn 1984, Dr. Daniel Drucker, an endocrinologist from the University of Toronto, discovered a hormone that helped pave the way for popular diabetes drugs such as Ozempic.