Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. Bruno Correia Sergey Ovchinnikov biorxiv.org/content/10.110…

ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation 1. ImmunoStruct is a novel deep-learning model that integrates protein sequence, 3D structure, and biochemical properties for improved prediction

Congratulations to Kevin Bijan Givechian for developing this fantastic tool, #ImmunoStruct, a deep-learning model that integrates sequence/structural/biochemical information to predict immunogenicity of peptides presented by MHC class I molecules! Krishnaswamy Lab Etienne Caron

Check out our Immunostruct multimodal network that uses sequence, structure and biochemical properties for predicting the immunogenecity of peptides presented by MHC class I molecules---potentially for cancer vaccine design. Study lead by Kevin Bijan Givechian and Joao, joint students

Yale’s ImmunoStruct model combines protein data to better predict immune responses for infections and cancer, outperforming older models with 27,000 sample tests and lab validation. biorxiv.org/content/10.110…

Come say hello if you’re here at MIT MoML!

Thank you to all who joined us @ #MoML2024! Here's to another year of record-breaking attendance & incredible posters! Thanks to J&J, Takeda, Genesis Therapeutics, & Dimension for making MoML possible! Congrats again to Soojung Yang & Juno Nam on winning the Best Paper Prize!

A nice summary of some of our recent work building the ImmunoStruct model for immunogenicity prediction with Krishnaswamy Lab & Prof. Akiko Iwasaki - feel free to reach out with q’s!

ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation. Prof. Akiko Iwasaki Etienne Caron Kevin Bijan Givechian 📜Paper: biorxiv.org/content/10.110… #Immunogenicity #DeepLearning #CancerNeoepitopes

A great highlight of our recent work by Yexin Yang et al in the Science Magazine newsletter, written by Christie Wilcox, "Ghosts of viruses past could point to a way of combating all sorts of viruses" 👻 Link to our original paper here science.org/doi/10.1126/sc… Newsletter here

Today in #preprinthub2 Yee Kwan Law & Animesh Awasthi CeMM will discuss a #preprint from Kevin Bijan Givechian, Smita Krishnaswamy lab and Prof. Akiko Iwasaki on ImmunoStruct, a method for peptide immunogenicity prediction👏🤩🧑‍💻 Read the preprint here👇 biorxiv.org/content/10.110…

De novo binders for pMHC-1 complexes I particularly like this work because it answers two questions I often have about de novo binders: 1) Does this unlock a new set of targets? 2) Why can't we just use antibodies? pMHC-1 is a key target class that we're just starting to crack

Introducing ESM Cambrian. Unsupervised learning can invert biology at scale to reveal the hidden structure of the natural world. We’ve scaled up compute and data to train a new generation of protein language models. ESM C defines a new state of the art for protein

De novo design of high-affinity single-domain antibodies 1. The study introduces "EvolveX," a computational pipeline for de novo design of high-affinity single-domain antibodies (VHHs), capable of targeting predefined epitopes with remarkable precision and stability. 2. EvolveX

Was fun to reflect on this amazing work from the Dyno Therapeutics, Inc. team in the past year. We often cover our capsid results, and sometimes we write ML papers. This post is connecting the dots between our ML work and its impact in physical experiments. Here, GPUs and rigorous modeling

Some people today are discouraging others from learning programming on the grounds AI will automate it. This advice will be seen as some of the worst career advice ever given. I disagree with the Turing Award and Nobel prize winner who wrote, “It is far more likely that the

Join us PhD thesis defense #11 from our lab, joint with Prof. Akiko Iwasaki --- Kevin Bijan Givenchian! Reception afterwards!

Come join today! With Krishnaswamy Lab and Prof. Akiko Iwasaki

Congrats Kevin Bijan Givechian !