Jared Adolf-Bryfogle

Associate Director at J&J Innovative Medicine. Hardcore video gamer. Explorer. Inventor. Dreamer...

[Jared Adolf-Bryfogle @jadolfbr]

@SharQureshi1 @fluid_xr Right - I should have been more specific. I have many Q2s and Q3s. I mean what is it helping you with? Is there an app that you are using for a notebook or pipetting? Have spent many a year in the wet lab and to me, pipetting and being precise would be fairly difficult in M now

[Tyler Benster @tbenst]

RIP NIH—not only did the director of the NIH resign today, but the website https://t.co/PaGye1TXDA is down. PubMed, one of the world’s most valuable repositories of medical knowledge, is also down.

[Jared Adolf-Bryfogle @jadolfbr]

Ransacking of all of it (data) and then saying everyone who wants to can leave is some fucked up shit…

[Martin Pacesa @MartinPacesa]

Just before the New Year: BindCraft v1.5! Please fill out this form to request new features and help us make BindCraft even better.
https://t.co/J71Y2x5efd

[Biology+AI Daily @BiologyAIDaily]

Applying computational protein design to engineer affibodies for affinity-controlled delivery of vascular endothelial growth factor and platelet-derived growth factor

1. This study demonstrates how computational protein design can create affibodies for targeted and tunable delivery of VEGF and PDGF, addressing key challenges in angiogenesis and tissue repair.

2. Eight new affibodies were engineered with dissociation constants ranging from nanomolar to micromolar, enabling precise control of protein release kinetics for therapeutic applications.

3. Combining yeast surface display with computational modeling allowed the development of VEGF- and PDGF-specific affibodies with enhanced specificity and affinity tunability.

4. Affibody-conjugated hydrogels prolonged VEGF and PDGF bioactivity over seven days, surpassing non-affibody hydrogels in both sustained release and bioactivity.

5. Experimental validation showed that engineered affibodies modulate protein bioactivity, influencing VEGF-induced endothelial cell proliferation and PDGF-responsive fibroblast activity.

6. Rationally designed mutations via Rosetta modeling expanded affinity ranges and maintained specificity, showcasing the power of in silico design for biomaterials innovation.

7. The platform highlights a scalable approach to affinity-controlled protein delivery, with potential to revolutionize therapeutic angiogenesis and biomaterials-based protein therapies.

@mhhettiaratchi @ParisaH_Lab @karlymeifear @JonDorogin
📜Paper: https://t.co/G2POQzXYui

#ProteinDesign #Biomaterials #Angiogenesis #VEGF #PDGF

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio That and I think the more native-like structures that bindcraft can produce.

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio 3/n. I think bindcraft creates more native like proteins and these proteins are more dynamic than typical rock binders. I think this intrinsic dynamics actually play a huge role. dG is enthalpy (static) and entropy - maybe it’s this?

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio I don’t think at this point there is a good proxy for binding. I have heard some using scores from OpenMM to help, but I have yet to find a reliable method for binding affinity prediction. Binding is not just static structures - entropy plays a huge role.

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio There are more filters in bindcraft as well. InterfaceAnalzer is one of them. Many other Rosetta filters too. I think they all play a role. kD is hard to predict, in my experience I usually have used the interface score to rank designs and use iPTM/PTM, plDDT monomer, etc.

[Possu Huang Lab @PossuHuangLab]

1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens

TRACeR for MHC-I: https://t.co/AGzIC4Ooun
TRACeR for MHC-II: https://t.co/U4lRENyrGu

@HaotianDu4 @ljjchem @SgourakisLab @StanfordBiosci @UPennAllergyImm @CHOP_Research

[Sam Tipps @SamTipps]

Best read of the day - innovative design, and great science to generate large virus-like protein cages by breaking symmetry 🎉

https://t.co/TLyWPlGWwj

https://t.co/L7NYulQZrt

https://t.co/wXq5lsSzHt

Quinton Dowling,
@lsmin0152
@kribler
@KingLabIPD
@UWproteindesign

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio *many have been shown - but not in a single place or paper and very anecdotally

[Jared Adolf-Bryfogle @jadolfbr]

@btnaughton @rohitsingh8080 @adaptyvbio All these have been shown to not directly correlate with KD. But it’s certainly worth trying on larger data sets like this. Maybe try InterfaceAnalyzer from PyRosetta. Still better as a filter or selector, but may have some correlation here - esp with nonbinders

[Ron Alfa @Ronalfa]

Announcing OCTO-VirtualCell (vc) a multi-scale, multimodal transformer trained to predict gene expression for a virtual cell in cellular contexts within patient tissue samples. Complete wth the Celleporter demo app to explore the data!

1/

[Amir Shanehsazzadeh @amirshanehsaz]

We @abscibio are excited to open source the code and datasets for IgDesign, with over 1,000 SPR datapoints against 7 targets! https://t.co/Qzl7nW4Pzk

With these data, we benchmark the ability of folding models to predict binding. More details below and in https://t.co/z5x5AIgolr

[Jared Adolf-Bryfogle @jadolfbr]

@GreenHellVR PCVR??

[Gabriele Corso @GabriCorso]

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with @jeremyWohlwend, @pas_saro and an amazing team at MIT and Genesis Therapeutics. A thread!

[Pushmeet Kohli @pushmeet]

The #AlphaFold 3 model code and weights are now available for academic use. We @GoogleDeepMind are excited to see how the research community continues to use AlphaFold to address open questions in biology and new lines of research.

https://t.co/kVB9hWJZTI

[Boston Protein Design and Modeling Club @ProteinBoston]

Can't get enough protein design after the @NobelPrize last week? Then come see @ProfBuehlerMIT on Wednesday, October 23rd 2024 at 7pm EDT in Room 181, Building 68 @MIT

"Physics-aware agentic artificial intelligence to model, design and discover proteins"
https://t.co/E8bDyGzirb