Bryan Briney
@bryanbriney
Followers
578
Following
134
Media
1
Statuses
699
Associate Professor at Scripps Research, studying antibody responses to immunization and infection. Big fan of open science and dogs.
San Diego, CA
Joined May 2009
I’m excited to share Profluent-E1, our internal encoder model for protein sequences, with the protein-ML community! The E1 series of models can be used as a drop-in replacement to upgrade a broad range protein modeling and design of workflows. https://t.co/r0sIXrVvBT
biorxiv.org
Large language models trained on natural proteins learn powerful representations of protein sequences that are useful for downstream understanding and prediction tasks. Because they are only exposed...
4
12
117
Spontaneous Emergence of Symmetry in a Generative Model of Protein Structure 1. A new study reveals that a transformer-based generative model can spontaneously generate symmetric protein structures without explicit symmetry constraints. This is a significant breakthrough in
1
3
8
Glad to see our antibody design paper finally out in @Nature (and congrats to lead authors and everyone involved )! At @Xaira_Thera we are excited about pushing antibody design further to bind harder targets and make drugs for unmet medical needs. Paper: https://t.co/h2bXGOvuGW
2
48
300
The @NIH has awarded a $6.9M grant to Scripps Research scientists led by Bryan Briney, PhD (@bryanbriney), with Renan de Carvalho, PhD (@deCarvalhoRenan), Andrew Ward, PhD (@WardLab1), and Darrell Irvine, PhD, to uncover how HIV vaccines can generate long-lasting immune
0
4
9
Most metaphors in biology are qualitative and vague. "DNA is the blueprint of the cell." OK but, like, how big is that blueprint? For our latest essay, @ClamonsSam gives a bunch of QUANTITATIVE metaphors to help you understand the sizes of biology, from molecules to cells. He
3
24
105
Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬
8
40
294
Nature research paper: Nanobody-based recombinant antivenom for cobra, mamba and rinkhals bites https://t.co/MIaU0hD3W0
nature.com
Nature - A recombinant antivenom composed of eight nanobodies provides broad protection against venom-induced lethality and dermonecrosis in mice challenged with venoms from cobras, mambas and...
2
34
147
Does anyone have any guesses for why AF3 is just better than all its competitors across the board, even with the same exact architecture & training data? Is it nothing more than Google-sized training budget?
OF3p is already quite good. For any modality, it is comparable (or better) to the best existing OSS model for that modality. On RNA, where we spent considerable effort, it is at AF3-parity. RNA is a challenging modality where all models (incl AF3) leave much room for improvement.
10
3
59
Structure-guided design of native-like HIV Env Single Chain Trimers for enhanced stability, immunogenicity, and versatile vaccine delivery https://t.co/X0LWBwsXML
#biorxiv_immuno
biorxiv.org
Stabilizing the HIV envelope (Env) trimer in its native prefusion conformation is key to eliciting broadly neutralizing antibodies (bnAbs). We present a generalizable single-chain trimer-(SCT) design...
0
4
7
GhostFold: Accurate Protein Structure Prediction Using Structure-Constrained Synthetic Coevolutionary Signals 1. GhostFold introduces a novel method for protein structure prediction that generates synthetic multiple sequence alignments (MSAs) from a single amino acid sequence,
0
8
49
Our GhostFold manuscript is up on bioRxiv, just in time for Halloween! https://t.co/sHrhHyneSg
biorxiv.org
The accuracy of protein structure prediction models such as AlphaFold2 is tightly coupled to the depth and quality of multiple sequence alignments ( MSAs ), posing a persistent challenge for proteins...
0
0
1
Legend has it gym memberships are particularly hard to cancel here because nobody knows how to exit
294
817
11K
Most AF3 demos skipped glycans. JAAG removes a bottleneck: SugarDrawer/GlycoCT → BAP+CCD JSON, sequon tagging + smart userCCD for sialyl / sulfated / phosphorylated links.
1
1
1
A Single-Cell Atlas of Transcriptional and Immunoglobulin Repertoire Evolution in Early B Cell Development https://t.co/NL4qPbadLi
#biorxiv_immuno
biorxiv.org
The development of human B cells in the bone marrow can be separated into functionally and transcriptionally distinct subsets, which while canonically described have yet to be profiled deeply and...
0
2
5
did you mean... π-thon?
Python 3.14 stable dropped today! Congratulations to everyone involved. You can install it now with `uv python upgrade 3.14`.
37
653
8K
AlphaFoldDB updated, now includes the MSAs 🥳
We’re renewing our collaboration with @GoogleDeepMind! We'll keep developing the AlphaFold Database to support protein science worldwide 🎉 To mark the moment we’ve synchronised the database with UniProtKB release 2025_03 https://t.co/VTzPuEUC1r
#AlphaFold
4
46
343
Has anyone even asked the cells if they wish to be perturbed
7
19
238
Antibody design may be just about to leave its “spray‑and‑pray" era. Chai‑2 reports ~50% de‑novo hits incl. sub‑nM. IgGM, Germinal, PXDesign join the push. Mosaic + AIntibody/BenchBB makes it testable. The bottleneck seems to be clean affinity data.
2
17
88
We’re recruiting a PhD Fellow in Computational Systems Immunology. Work on large-scale immune receptor datasets and develop computational models in close collaboration with experimental labs. Apply here:
0
4
8