molecular-dynamics
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| Title | Date |
|---|---|
| Ookami Webinar | 02/14/24 |
| Request for Proposals for Anton 2 | 05/09/23 |
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Knowledge Base Resources
| Title | Category | Tags | Skill Level |
|---|---|---|---|
| CHARMM Links to Install, Run, and Troubleshoot MD Simulations | Learning | charmm, molecular-dynamics, namd, computational-chemistry | Beginner, Intermediate |
| Molecular Dynamics Tutorials for Beginner's | Learning | cloud-computing, amber, charmm, gromacs, molecular-dynamics, namd, computational-chemistry | Beginner |
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:
- 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.
Status: In Progress
People with Expertise
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Bala Desinghu
Harvard University
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ACCESS CSSN, Campus Champions, CAREERS, Northeast
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mentor, researcher/educator, research computing facilitator, cssn, Consultant
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Lisa Perez
Texas A&M University
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SWEETER, ACCESS CSSN
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research computing facilitator, cssn, Affinity Group Leader
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