molecular-dynamics
Mentors and Regional Facilitators
| Name | Region | Skills | Interests |
|---|---|---|---|
| Aya Nawano | CAREERS, ACCESS CSSN | ||
| Bala Desinghu | ACCESS CSSN, Campus Champions, CAREERS, Northeast | ||
| 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
Xiaoqin Huang
Rice University
Programs
ACCESS CSSN
Roles
mentor, research computing facilitator, research software engineer, cssn
Expertise
Expertise
Sebastian Sensale
Cleveland State University
Programs
Campus Champions
Roles
research computing facilitator
Expertise
People with Interest
Interests
Mark Perri
Sonoma State University
Programs
Campus Champions
Roles
researcher/educator, research computing facilitator
Interests