本文へ移動
cccskills
無料GitHub で公開

aav-vector-design-agent

AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.

bg-szy/TOP-SKILLS
インストール方法を見る

含まれるファイル（1）

  • SKILL.md5.8 KB

SKILL.md（原文）

インストールする前に、エージェントに与えられる指示の中身を確認できます。

<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

AAV Vector Design Agent

The AAV Vector Design Agent provides AI-driven design of adeno-associated virus vectors for gene therapy applications. It covers capsid selection and engineering, promoter/enhancer design, transgene optimization, and manufacturing considerations.

When to Use This Skill

  • When selecting optimal AAV serotype for tissue-specific targeting.
  • To design novel capsid variants with enhanced properties.
  • For optimizing transgene expression cassettes.
  • When predicting immunogenicity and neutralizing antibody escape.
  • To design liver-detargeted or CNS-tropic vectors.

Core Capabilities

  1. Capsid Selection: Match AAV serotype to target tissue based on tropism profiles.

  2. Capsid Engineering: Design modified capsids for enhanced transduction or immune evasion.

  3. Promoter Design: Select and optimize tissue-specific or ubiquitous promoters.

  4. Transgene Optimization: Codon optimization and regulatory element design.

  5. Immunogenicity Prediction: Predict NAb binding and T-cell epitopes.

  6. Manufacturing Assessment: Evaluate producibility and purification considerations.

AAV Serotype Tropism

SerotypePrimary TropismClinical Use
AAV1Muscle, CNSGlybera (muscle)
AAV2Broad (liver, muscle)Luxturna (retina)
AAV5CNS, liver, retinaHemgenix (liver)
AAV8Liver, muscleMultiple trials
AAV9CNS, cardiac, liverZolgensma (CNS)
AAVrh10CNS, liverCNS trials
AAVrh74MuscleElevidys (muscle)
AAV-PHP.eBCNS (mouse)Research

Workflow

  1. Input: Target tissue, therapeutic gene, patient population characteristics.

  2. Capsid Selection: Rank serotypes by tropism profile match.

  3. Capsid Engineering: Design modifications if needed (peptide insertion, point mutations).

  4. Cassette Design: Optimize ITR-to-ITR expression cassette.

  5. Immunogenicity Analysis: Predict NAb prevalence and T-cell epitopes.

  6. Manufacturing Review: Assess production feasibility.

  7. Output: Complete vector design with rationale.

Example Usage

User: "Design an AAV vector for liver-directed gene therapy in hemophilia B with low immunogenicity."

Agent Action:

python3 Skills/Gene_Therapy/AAV_Vector_Design_Agent/aav_designer.py \
    --target_tissue liver \
    --therapeutic_gene F9 \
    --indication hemophilia_b \
    --minimize_immunogenicity true \
    --nab_escape true \
    --promoter liver_specific \
    --output aav_design/

Expression Cassette Components

5' ITR - [Promoter] - [5' UTR] - [Transgene] - [WPRE] - [PolyA] - 3' ITR

Packaging limit: ~4.7 kb between ITRs

Promoter Options:

PromoterTypeSizeApplication
CAGUbiquitous1.7 kbStrong expression
EF1αUbiquitous1.2 kbConstitutive
LP1Liver-specific0.5 kbHepatocyte targeting
hSynNeuron-specific0.5 kbCNS applications
MCKMuscle-specific0.6 kbMyopathies
CMVUbiquitous0.6 kbHigh initial (silenced)

Capsid Engineering Strategies

Directed Evolution:

  • Error-prone PCR libraries
  • DNA shuffling
  • Selection in target tissue

Rational Design:

  • Peptide display (insertion in variable loops)
  • Point mutations for receptor targeting
  • Tyrosine-to-phenylalanine for stability

Machine Learning:

  • Sequence-function models
  • Generative models for novel capsids
  • Tropism prediction

Immunogenicity Considerations

Pre-existing NAbs:

SerotypeNAb Prevalence
AAV230-60%
AAV515-30%
AAV815-25%
AAV920-35%

Mitigation Strategies:

  • Serotype selection based on patient screening
  • Engineered NAb-evading capsids
  • Immunosuppression protocols
  • Plasmapheresis

AI/ML Components

Tropism Prediction:

  • CNN on capsid sequence
  • Cell-type specific transduction
  • Cross-species translation

Immunogenicity Modeling:

  • MHC binding prediction
  • T-cell epitope mapping
  • NAb epitope prediction

Expression Optimization:

  • Codon optimization algorithms
  • RNA structure prediction
  • miRNA target site avoidance

Manufacturing Considerations

FactorImpactOptimization
Capsid yieldProduction costSequence modifications
Empty/full ratioPotencyPurification method
AggregationStabilityFormulation
DNA packagingTransgene sizeCassette design

Prerequisites

  • Python 3.10+
  • Sequence analysis tools
  • Immunoinformatics packages
  • Structural biology tools

Related Skills

  • CRISPR_Design_Agent - For gene editing payloads
  • Protein_Engineering - For capsid design
  • RNA_Therapeutics - For alternative modalities

Regulatory Considerations

  1. Biodistribution: Required for IND
  2. Shedding: Vector in bodily fluids
  3. Germline transmission: Gonadal presence
  4. Integration risk: Random vs site-specific
  5. Immunogenicity: Pre-existing and induced

Author

AI Group - Biomedical AI Platform

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

レビュー

まだレビューはありません。使ってみた感想をお寄せください。

ログインしてレビューを書く

同じリポジトリのスキル

概要と使いどころ

academic-humanizer

無料

Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

academic-paper

無料

12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견 반영, 답변서 점검, AI 사용 고지.

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

academic-paper-composer

無料

Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

academic-paper-reviewer

無料

Multi-perspective academic paper review with dynamic reviewer personas. Runs a 5-seat, role-separated review panel (Journal-Fit Reviewer + 3 peer-review roles + Devil's Advocate) with field-specific expertise; role separation is not a claim of independent error processes. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy, 審查論文, 論文審查, 模擬審查, 同儕審查, 幫我審這篇, 以審查人角度評估, 審查者校準, 논문 심사, 동료 심사, 모의 심사, 심사자 관점에서 평가, 심사자 보정.

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

academic-paper-strategist

無料

Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

academic-pipeline

無料

Orchestrator for the full academic research pipeline: research -> write -> integrity check -> review -> revise -> re-review -> re-revise -> final integrity check -> finalize. Coordinates deep-research, academic-paper, and academic-paper-reviewer into a seamless 10-stage workflow with mandatory, coverage-bounded integrity checks, two-stage peer review, and auditable quality-assurance artifacts. Triggers on: academic pipeline, research to paper, full paper workflow, paper pipeline, end-to-end paper, research-to-publication, complete paper workflow, 연구부터 논문까지, 연구 주제 설정부터 논문 완성까지, 논문 전체 워크플로.

日本語の概要は準備中です。原文の説明を表示しています。

bg-szy/TOP-SKILLS62026年9月8日 更新

bg-szy のスキルをすべて見る

このスキルの問題を報告する