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Title Date
Ookami Webinar 02/14/24

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Knowledge Base Resources

Title Category Tags Skill Level
Attention, Transformers, and LLMs: a hands-on introduction in Pytorch Learning aideep-learningmachine-learning +2 more tags Intermediate
DeepChem Tool pytorchtensorflowcomputational-chemistry Beginner, Intermediate, Advanced
fast.ai Website aimachine-learningpytorch +1 more tags Beginner, Intermediate, Advanced

Engagements

Re-engineering Lilly’s KisunlaTM into a novel antibody targeting IL13RA2 against GBM using AI-driven macromolecular modeling
Atrium Health Levine Cancer
  • 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.
Status: In Progress

People with Expertise

Adham Khalifa

Connecticut College

Programs

CAREERS

Roles

student-facilitator

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Expertise

Swabir Silayi

George Mason University

Programs

ACCESS CSSN, CCMNet, Campus Champions

Roles

mentor, research computing facilitator, cssn, Consultant, CCMNet

Expertise

shuai liu

University of Arkansas

Programs

ACCESS CSSN

Roles

research computing facilitator

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Expertise

People with Interest

Russell Hofmann

Internet2

Programs

ACCESS CSSN, CCMNet

Roles

mentor, cssn, CCMNet

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Interests

Ana Marija Sokovic

University of Illinois at Chicago

Programs

CCMNet

Roles

CCMNet

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Interests

+69 more tags

Shawn Sivy

The College of New Jersey

Programs

Campus Champions, CAREERS

Roles

research computing facilitator, ci systems engineer

Interests