molecular-dynamics
Mentors and Regional Facilitators
| Name | Region | Skills | Interests |
|---|---|---|---|
| Aya Nawano | CAREERS, ACCESS CSSN | ||
| Bala Desinghu | ACCESS CSSN, Campus Champions, CAREERS, Northeast | ||
| Daniel Benedict | CCMNet | ||
| Deborah Penchoff | Campus Champions | ||
| Jacob Pessin | Northeast | ||
| Juan Vanegas | Northeast | ||
| Jason Key | Campus Champions | ||
| Od Odbadrakh | ACCESS CSSN | ||
| Lisa Perez | SWEETER, ACCESS CSSN | ||
| Nannan Shan | CCMNet, ACCESS CSSN | ||
| Paul Rulis | Campus Champions | ||
| Russell Hofmann | ACCESS CSSN, CCMNet | ||
| Xiaoqin Huang | ACCESS CSSN | ||
| Swabir Silayi | ACCESS CSSN, CCMNet, Campus Champions | ||
| Sebastian Sensale | Campus Champions | ||
| Thomas Cheatham | Campus Champions, RMACC |
Affinity Groups
There are no Affinity Groups associated with this topic. View All 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
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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
Expertise
Lisa Perez
Texas A&M University
Programs
SWEETER, ACCESS CSSN
Roles
research computing facilitator, cssn, Affinity Group Leader
Expertise
Expertise
People with Interest
Mark Perri
Sonoma State University
Programs
Campus Champions
Roles
researcher/educator, research computing facilitator
Interests
Bala Desinghu
Harvard University
Programs
ACCESS CSSN, Campus Champions, CAREERS, Northeast
Roles
mentor, researcher/educator, research computing facilitator, cssn, Consultant
Interests
Daniel Morales
Florida International University
Programs
Campus Champions
Roles
research computing facilitator, student champion
