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## APPLICATION OVERVIEW
This web application aims to provide a platform for bioinformatics analysis, focusing on molecular docking and stimulation. Users will be able to upload ligand and receptor files, select appropriate software for docking (PyRx, AutoDock, or Vina), and download the results in the desired file format. The application will serve as a comprehensive tool for researchers in the bioinformatics field, streamlining complex analysis tasks.

## CORE FEATURES
1. **File Upload**: Users can upload ligand and receptor files for molecular docking analysis.
2. **Software Selection**: A feature that allows users to choose the docking software (PyRx, AutoDock, or Vina) before proceeding with the analysis.
3. **File Format Options**: Users can select the desired output file type for their docking results, ensuring compatibility with the chosen software.
4. **Results Viewer**: After processing, users can view and download their docking results directly from the platform.
5. **Bioinformatics Tools Library**: A section that lists various bioinformatics tools and techniques available for exploration and education.
6. **Contact Form**: A feature for users to reach out for support or inquiries about the application or bioinformatics services.

## DESIGN SPECIFICATIONS
- **Visual Style**: minimalist - Clean, simple design with plenty of white space, minimal color palette, and focus on typography
- **Color Mode**: Light theme with dark text on light backgrounds
- **Primary Color**: #1978E5 (accent for buttons, links, highlights)
- **Typography**: Use Inter from Google Fonts for headings, Inter for body text and UI elements
- **Border Radius**: 8px (moderately rounded) for buttons, cards, and inputs
- **Layout**: The main layout will feature a top navigation bar, a hero section with a call-to-action, followed by sections for features, a results area, and a contact form.

## TECHNICAL REQUIREMENTS
- **Framework**: React with TypeScript
- **Styling**: Tailwind CSS
- **UI Components**: shadcn/ui
- **State Management**: Redux or Context API (if needed)

## IMPLEMENTATION STEPS
1. Set up a new React project with TypeScript and install required dependencies (React, Tailwind CSS, shadcn/ui).
2. Create the main layout structure, including a navigation bar and footer.
3. Implement the file upload component allowing users to upload ligand and receptor files.
4. Develop the software selection dropdown and output file type options.
5. Create the results viewer to display and enable downloads of the docking results.
6. Add a library section that outlines various bioinformatics tools available.
7. Implement the contact form allowing users to submit inquiries.
8. Ensure responsive design for optimal viewing on various devices.
9. Conduct testing to ensure all functionalities are working as intended.
10. Deploy the application on a suitable platform (e.g., Vercel, Netlify).

## USER EXPERIENCE
Users will interact with the application by first navigating to the site and viewing the hero section, which provides an overview of the application's purpose. They can then upload their files, choose their preferred software, and select the file format for their results. After submitting, users will be directed to a results page where they can download their analysis. The application will also provide educational resources about bioinformatics tools and prompt users to contact support for further assistance if needed. The overall design will ensure a smooth and intuitive user experience, focusing on ease of navigation and interaction.