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Knowledge Base Resources

Title Category Tags Skill Level
A guide to pip in Python Learning pipsoftware-installation Beginner, Intermediate
Installing Rocky Linux Operating System Learning unix-environmentsoftware-installation Beginner
Neurodesk Website psychologycontainerssoftware-installation +1 more tags Beginner, Intermediate, Advanced

Engagements

Modelling conformational heterogeneity for human glutamine synthetase variants
San Francisco State University

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

Status: Recruiting
Re-engineering Lilly’s KisunlaTM into a novel antibody targeting IL13RA2 against GBM using AI-driven macromolecular modeling Active
Atrium Health
  • 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: Recruiting

People with Expertise

Timothy Middelkoop

Internet2

Programs

ACCESS CSSN, Campus Champions, CCMNet, Great Plains

Roles

mentor, regional facilitator, researcher/educator, research computing facilitator, CCMNet

Timothy Middelkoop (white male with short dark hair and glasses, he/him,his)

Expertise

Feseha Abebe-Akele

Elizabeth City State University

Programs

CCMNet

Roles

mentor, researcher/educator, research computing facilitator, CCMNet

Feseha Abebe-Akele

Expertise

Jeremy Schafer

Rutgers, the State University of New Jersey

Programs

CCMNet

Roles

CCMNet

Placeholder headshot

Expertise

People with Interest

Natasha Pavlovikj

University of Nebraska, Lincoln

Programs

CCMNet, Campus Champions

Roles

mentor, researcher/educator, research computing facilitator, CCMNet

Placeholder headshot

Interests

Widodo Samyono

Jarvis Christian College

Programs

Campus Champions, CCMNet

Roles

researcher/educator, research computing facilitator, CCMNet

Widodo Samyono, PhD in Computational and Applied Mathematics

Interests

Sapana Soni

LBNL

Programs

CCMNet

Roles

CCMNet

Placeholder headshot

Interests