deployment
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| Title | Category | Tags | Skill Level |
|---|---|---|---|
| Containerized Jupyter Notebooks for HPCs | Learning | cloud, cloud-computing, openstack, scratch, data-management, data-reproducibility, github, workflow, open-ondemand, administering-hpc, configuration-automation, hpc-getting-started, hpc-tools, deployment, scripting, conda, jupyterhub, programming-best-practices, python, mpi, containers, docker, singularity | Intermediate |
Engagements
Re-engineering Lilly’s KisunlaTM into a novel antibody targeting IL13RA2 against GBM using AI-driven macromolecular modeling
- Summary and objectives of the proposed experiments:
- 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.
- 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.
- Modify, improve, and optimize the overall or full antibody protein structures using AI-driven macromolecule modeling (AlphaFold3).
- 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.
People with Expertise
Cody Stevens
Wake Forest University
Programs
Campus Champions, CCMNet
Roles
regional facilitator, researcher/educator, research computing facilitator, ci systems engineer, CCMNet
Expertise
Michael Blackmon
Davidson College
Programs
Campus Champions, ACCESS CSSN
Roles
mentor, research computing facilitator, ci systems engineer, cssn
Expertise
Charles Forsyth
University of California, Riverside
Programs
Campus Champions
Roles
regional facilitator, research computing facilitator
Expertise
People with Interest
Matthew Chung
University of California, Riverside
Programs
ACCESS CSSN, CCMNet
Roles
research computing facilitator, ci systems engineer, cssn, CCMNet
Interests
William Lai
Cornell University
Programs
ACCESS CSSN
Roles
mentor, researcher/educator, research computing facilitator, research software engineer, ci systems engineer, Consultant
Interests
Timothy Middelkoop
Internet2
Programs
ACCESS CSSN, Campus Champions, CCMNet, Great Plains
Roles
mentor, regional facilitator, researcher/educator, research computing facilitator, CCMNet
