Engagements tagged generative-ai

• Summary and objectives of the proposed experiments: 

1. An initial research-based Ab (scFv47, discovered by our collaborator Dr. Balyasnikova) model, modeling Ab-Ag (IL13RA2 against GBM) protein complex, and identifying the binding sites (epitopes) using ROSETTA and AlphaFold2 multimer tools.
2. Graft the CDRs of scFv (single-chain variable fragment) of antibody or Bispecific T cell engagers (BTEs) onto the template Ab, the framework of Lilly's Kisunla™ Ab drug.
3. Modify, improve, and optimize the overall or full antibody protein structures using AI-driven macromolecule modeling (AlphaFold3).
4. Explore single nucleotide polymorphism (SNP), pathogenic genetic variants and N-glycosylation of IL13RA2 (target) protein domain interacting with the Ab candidates among the patient population using ROSETTA software packages.

In this project, our primary goal is to develop a multimodal foundation model of the brain by combining large-scale, self-supervised learning with the IBL brainwide dataset. This model aims to serve as a "universal translator," facilitating automatic translation from neural activity to various outputs such as behavior, brain location, neural dynamics prediction, and information flow prediction. To achieve this, we will leverage ACCESS computational resources for model training, fine-tuning, and testing. These resources will support the computation-intensive tasks involved in training large-scale deep learning models on distributed GPUs, as well as processing and analyzing the extensive dataset. Additionally, we will utilize software packages tailored for deep learning to implement our algorithms and models effectively. Ultimately, the project's outcome will be shared as an open-source model, serving as a valuable resource for global neuroscience research and the development of brain-computer interfaces. With ACCESS resources, we aim to accelerate the advancement of neuroscience and enable broader participation in brain-related research worldwide.