I am pleased to announce the release of ProteinDJ v2! This is a major update that integrates BindCraft into the pipeline as an alternative to RFdiffusion for binder generation. You can try it out here: github.com/PapenfussLab/proteindj
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social

Evaluating BindCraft for Generative Design of High-Affinity Peptides Discovering high-affinity ligands directly from protein structures remains a key challenge in drug discovery. BindCraft is a structure-guided generative modeling platform able to de novo design miniproteins with a high affinity for a large set of targets. While miniproteins are valuable research tools, short peptides offer substantially greater therapeutic potential. However, given their lack of stabilized tertiary structures, de novo generation of functional peptides is a remarkable challenge. Here, we show that BindCraft is able to generate high affinity peptides, solely based on target structure, with remarkable success rates. For the oncoprotein MDM2, BindCraft generated 70 unique peptides; 15 were synthesized, and 7 showed specific binding with nanomolar affinities. Competition assays confirmed site-specific binding for the intended target site. For another oncology target, WDR5, six out of nine candidates bound the MYC binding WBM site with submicromolar affinity. Bindcraft’s high fidelity structure prediction enabled one shot peptide optimization via rational chemical modification, improving the potency of one WDR5 binder by 6-fold to a KD of 39 nM. BindCraft also generated candidate peptides for targeting PD-1 and PD-L1. However, none of the tested peptides showed detectable binding. Together, these results establish a first evaluation of BindCraft for peptide binder prediction. Despite remaining limitations, this tool shows the potential to rival display technologies in delivering high-affinity ligands for therapeutic development.

Looking for a high-affinity #peptide binder for your favorite target?

According to the newest paper by the group of @sebastianpomplun.bsky.social, the software tool #BindCraft allows you to predict such binders with high success rates.

pubs.acs.org/doi/10.1021/...
#ChemSky #ChemBio #DrugDiscovery

The award was primarily on the development of #BindCraft, membrane protein solubilisation, and structural characterization and engineering of gene editors.

An open-source AI platform to democratize protein design Since its release in 2024, the open-source platform BindCraft, developed at EPFL, has already disrupted the world of protein design. Physical interactions between proteins influence anything from…

Open-source #AI platform to democratize protein #design ...

| #BindCraft | #aminoacid | #virus | #binders | Via @sciencex.bsky.social

One-shot design of functional protein binders with BindCraft #bindcraft #protein #design #molecularmodeling #modeling #ppis #alphafold2

A collaborative team have published #BindCraft, an AI tool that designs powerful protein binders in one shot.
Critical for faster drugs, smarter diagnostics, and biotech breakthroughs ahead. www.nature.com/articles/s41...

#Bindcraft goes to Zurich!

schedule introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC!

Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu

"BindCraft: one-shot design of functional protein binders"

bpdmc.org

Protein Structure Viewer Upload and interactively visualize multiple Protein Data Bank (.pdb) structures.

Just made my first webapp mostly for analyzing structures from #BindCraft
👉🏼 pdb-viewer.lovable.app

It’s bare 🦴 at this point but curious if others find something like this useful and features they’d like?
🧬🧶

Thanks to @biancabroske.bsky.social , @scbinder.bsky.social , @tim-kempchen.bsky.social and all the other authors for a fantastic collaboration. A big thank you goes to the developers of #RFdiffusion, #Chroma, #Bindcraft and others to make these amazing algorithms available.

Text from an email about the status of a program.

An email I look forward to getting!
#BindCraft #ProteinDesign
Will have to optimize some settings to get more designs 💻

Synthetic Protein Interaction Project Recent machine learning-based methods - including RFdiffusion, FoldFlow-2 and BindCraft - now enable the de novo design of synthetic proteins that interact with any specific protein, nucleic acid, ...

@biogrid.bsky.social is happy to release of our new themed curation project on #SyntheticProtein interactions using proteins generated with #rfdiffusion, #foldflow, and #bindcraft. Our page linked below contains all interactions and download files will be available very soon 🧪 #AI #MachineLearning