Affinity Groups
Announcements
Title | Date |
---|---|
Ookami Webinar | 02/14/24 |
Request for Proposals for Anton 2 | 05/09/23 |
Upcoming Events & Trainings
Topics from Ask.CI
Knowledge Base Resources
Title | Category | Tags | Skill Level |
---|---|---|---|
CHARMM Links to Install, Run, and Troubleshoot MD Simulations | Learning | charmmmolecular-dynamicsnamd +1 more tags | Beginner, Intermediate |
Molecular Dynamics Tutorials for Beginner's | Learning | cloud-computingambercharmm +4 more tags | Beginner |
Engagements
Modelling conformational heterogeneity for human glutamine synthetase variants
Hi!
I want to use EMMIVox molecular dynamics based ensemble refinement to model into multiple cryoEM maps that my lab has generated. I am a collaborator of Max Bonomi (PI behind EMMIVox) but also want to be able to do this independently. We have pre-processed single-refinement models but need multiple GPUs to run the ensemble refinement. I am new to NSF ACCESS and also new to ensemble refinement/molecular dynamics in general. Specifically, I need help to:
- Allocate Resources (which is best/how much is needed)
- Software Installation (plumed dependencies and the software in the github link)
- Job running/management
I am running this part of the project myself and have not staffed this project yet with a student; so a mentor would be working directly with me. I would like assistance to run this procedure through at least once so that I can reach independence and start training my students to implement it.
Thank you so much in advance for any help and considering whether the MATCH+ program would be suitable for this project.
All the best,
Eric
Re-engineering Lilly’s KisunlaTM into a novel antibody targeting IL13RA2 against GBM using AI-driven macromolecular modeling Active
- 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.