My take on Modeling Large Amounts of HLA Molecules with Ruby

Understanding the 3D structures of HLA (human leukocyte antigen) molecules is crucial. These molecules help the immune system recognize what’s foreign and what’s not. Here’s why this matters:

Transplants: Matching HLA types between donors and recipi…


This content originally appeared on DEV Community and was authored by Mário Marroquim

Understanding the 3D structures of HLA (human leukocyte antigen) molecules is crucial. These molecules help the immune system recognize what's foreign and what's not. Here's why this matters:

  • Transplants: Matching HLA types between donors and recipients is key to avoid rejection.
  • Disease Links: Some HLA types are linked to autoimmune diseases, infections, and drug reactions.
  • Vaccines: Knowing how HLA presents antigens aids in designing effective vaccines.
  • Cancer Treatment: Identifying how HLA presents tumor antigens helps in personalized cancer therapies.

Ruby Script for HLA Modeling

Based on my previous work at pHLA3D, I developed a Ruby script to efficiently model large numbers of HLA molecules. Here's how it works:

  1. Data Prep: It gathers and preps HLA sequence data for analysis.
  2. Parallel Processing: It split the workload across multiple threads, cutting down processing time.
  3. ESMFold Integration: It uses Meta’s ESMFold online service, sending HLA sequences and getting back 3D models.
  4. Post-Processing: I intend to clean up and validate the models for further use. Can you help me with that?

Why This Rocks

  • Speed: Parallel processing handles data quickly.
  • Scalability: Using Meta's ESMFold means no need for a massive server setup.
  • Flexibility: Written in Ruby, this script is easy to tweak and expand.

In short, this approach makes modeling HLA molecules faster and more accessible, helping advance research and medical treatments. Please, contribute!


This content originally appeared on DEV Community and was authored by Mário Marroquim


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Mário Marroquim | Sciencx (2024-06-23T14:13:23+00:00) My take on Modeling Large Amounts of HLA Molecules with Ruby. Retrieved from https://www.scien.cx/2024/06/23/my-take-on-modeling-large-amounts-of-hla-molecules-with-ruby/

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