# r-akshai-kumar02/huntington-disease architecture

> Architecture diagram of the GitHub repository r-akshai-kumar02/huntington-disease, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-24). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/r-akshai-kumar02/huntington-disease
- Repository: https://github.com/r-akshai-kumar02/huntington-disease

## Overview

This repository documents an in-silico study of Juglans regia compounds against mutant huntingtin, rather than a conventional application. The documented workflow retrieves phytochemicals, screens their pharmacokinetic and toxicity properties, predicts pharmacodynamic activity, docks the passing compounds, and evaluates the Geranic acid complex with molecular dynamics. The tree exposes README files but no implementation source, so edges reflect only the workflow stated in the project description; paths for undocumented stages use their existing enclosing directories.

Main entry points: [`Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server`](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server) (ADMET and toxicity screening), [`Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server/Docking`](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server/Docking) (Comparative molecular docking), [`README.md`](https://github.com/r-akshai-kumar02/huntington-disease/blob/main/README.md) (Juglans regia compounds), [`Simulation`](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Simulation) (Molecular dynamics simulation)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_screening["Compound screening"]
  node_admet["ADMET and toxicity screening"]
  node_pass["PASS activity prediction"]
  node_selected["Six screened compounds<br/>[README.md]"]
end

subgraph group_structure["Structure evaluation"]
  node_docking["Comparative molecular docking"]
  node_interactions["Geranic acid interactions"]
  node_simulation["Molecular dynamics simulation"]
  node_stability["Complex stability assessment<br/>[README.md]"]
end

subgraph group_study["Study documentation"]
  node_juglans["Juglans regia compounds<br/>[README.md]"]
  node_report["Study findings<br/>[README.md]"]
end

node_researcher(("Researcher"))
node_bimp[("BIMP database")]
node_swissadme["SwissADME"]
node_protox["ProTox-3.0"]
node_passserver["PASS online server"]
node_vina["AutoDock Vina"]
node_libdock["LibDock"]
node_openmm["OpenMM"]

node_researcher -->|"studies"| node_juglans
node_bimp -->|"provides compounds"| node_juglans
node_juglans -->|"screened for properties"| node_admet
node_admet -.->|"uses"| node_swissadme
node_admet -.->|"uses"| node_protox
node_juglans -->|"assessed for activity"| node_pass
node_pass -.->|"uses"| node_passserver
node_admet -->|"selects six"| node_selected
node_selected -->|"compared by docking"| node_docking
node_docking -.->|"uses"| node_vina
node_docking -.->|"uses"| node_libdock
node_docking -->|"identifies interactions"| node_interactions
node_interactions -->|"evaluated by dynamics"| node_simulation
node_simulation -.->|"uses"| node_openmm
node_simulation -->|"assesses"| node_stability
node_stability -->|"informs"| node_report

click node_juglans "https://github.com/r-akshai-kumar02/huntington-disease/blob/main/README.md"
click node_admet "https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server"
click node_pass "https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server"
click node_selected "https://github.com/r-akshai-kumar02/huntington-disease/blob/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/README.md"
click node_docking "https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server/Docking"
click node_interactions "https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server/Docking"
click node_simulation "https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Simulation"
click node_stability "https://github.com/r-akshai-kumar02/huntington-disease/blob/main/Simulation/README.md"
click node_report "https://github.com/r-akshai-kumar02/huntington-disease/blob/main/README.md"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_admet,node_pass,node_selected toneBlue
class node_docking,node_interactions,node_simulation,node_stability,node_bimp toneAmber
class node_juglans,node_report,node_passserver toneMint
class node_researcher,node_swissadme,node_protox,node_vina,node_libdock,node_openmm toneIndigo
```

## Components

### Compound screening

- [ADMET and toxicity screening](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server): `Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server`
- [PASS activity prediction](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server): `Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server`
- [Six screened compounds](https://github.com/r-akshai-kumar02/huntington-disease/blob/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/README.md): `Pharmacokinetics and Pharmacodynamics Result/README.md`

### Structure evaluation

- [Comparative molecular docking](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server/Docking): `Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server/Docking`
- [Geranic acid interactions](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Pharmacokinetics%20and%20Pharmacodynamics%20Result/ADMET%20and%20Pass%20server/Docking): `Pharmacokinetics and Pharmacodynamics Result/ADMET and Pass server/Docking`
- [Molecular dynamics simulation](https://github.com/r-akshai-kumar02/huntington-disease/tree/main/Simulation): `Simulation`
- [Complex stability assessment](https://github.com/r-akshai-kumar02/huntington-disease/blob/main/Simulation/README.md): `Simulation/README.md`

### Study documentation

- [Juglans regia compounds](https://github.com/r-akshai-kumar02/huntington-disease/blob/main/README.md): `README.md`
- [Study findings](https://github.com/r-akshai-kumar02/huntington-disease/blob/main/README.md): `README.md`

### Other components

- **Researcher**
- **BIMP database**
- **SwissADME**
- **ProTox-3.0**
- **PASS online server**
- **AutoDock Vina**
- **LibDock**
- **OpenMM**

## Connections

- Researcher → Juglans regia compounds: studies
- BIMP database → Juglans regia compounds: provides compounds
- Juglans regia compounds → ADMET and toxicity screening: screened for properties
- ADMET and toxicity screening → SwissADME: uses
- ADMET and toxicity screening → ProTox-3.0: uses
- Juglans regia compounds → PASS activity prediction: assessed for activity
- PASS activity prediction → PASS online server: uses
- ADMET and toxicity screening → Six screened compounds: selects six
- Six screened compounds → Comparative molecular docking: compared by docking
- Comparative molecular docking → AutoDock Vina: uses
- Comparative molecular docking → LibDock: uses
- Comparative molecular docking → Geranic acid interactions: identifies interactions
- Geranic acid interactions → Molecular dynamics simulation: evaluated by dynamics
- Molecular dynamics simulation → OpenMM: uses
- Molecular dynamics simulation → Complex stability assessment: assesses
- Complex stability assessment → Study findings: informs