# Geometricus

> structure-based, alignment-free embedding approach for proteins

**Wikidata**: [Q114840743](https://www.wikidata.org/wiki/Q114840743)  
**Source**: https://4ort.xyz/entity/geometricus

## Summary
Geometricus is a software tool designed for protein analysis, functioning as a structure-based, alignment-free embedding approach. It allows users to process protein structures without relying on sequence alignment. The tool is open-source and accessible via a dedicated GitHub repository.

## Key Facts
- **Classification:** It is an instance of software.
- **Core Function:** Provides a structure-based, alignment-free embedding approach specifically for proteins.
- **License:** Distributed under the MIT License.
- **Source Code:** Hosted publicly at `https://github.com/TurtleTools/geometricus`.
- **Official Website:** Documentation and details are available at `https://turtletools.github.io/geometricus/`.
- **Latest Version:** Version 0.3.0 (released April 20, 2022).
- **Initial Release:** Versions 0.1.0, 0.1.1, and 0.1.2 were all released on September 6, 2020.

## FAQs
### Q: What is the primary function of Geometricus?
A: Geometricus is an approach used to generate embeddings for proteins based on their structure. It is distinguished by being "alignment-free," meaning it does not require sequence alignment to process protein data.

### Q: Is Geometricus free to use?
A: Yes, Geometricus is released under the MIT License, which is a permissive free software license allowing for broad reuse and modification.

### Q: When was the most recent update released?
A: The most recent preferred version listed is 0.3.0, which was released on April 20, 2022.

### Q: Where can the software be accessed?
A: The source code is available on GitHub at `https://github.com/TurtleTools/geometricus`, and additional information is hosted at `https://turtletools.github.io/geometricus/`.

## Why It Matters
Geometricus serves a specific niche in computational biology and bioinformatics by providing a method for protein analysis that bypasses the traditional constraints of sequence alignment. By using a structure-based approach, it allows for the comparison and embedding of proteins based on their three-dimensional physical properties rather than their linear genetic sequence. This is significant in scenarios where protein structures are known but sequences may be divergent or difficult to align accurately.

The tool's availability as open-source software under the MIT License ensures that it is accessible to the research community for verification, extension, and integration into larger bioinformatics pipelines. Its development history, spanning from September 2020 to April 2022, indicates ongoing maintenance and updates to its functionality, solidifying its role as a utility for structure-based protein embedding.

## Notable For
- **Methodology:** Being a structure-based, alignment-free embedding approach, distinguishing it from sequence-dependent tools.
- **Open Source:** Availability under the permissive MIT License.
- **Accessibility:** Hosting on GitHub under the "TurtleTools" organization.
- **Release Cadence:** Releasing multiple iterative versions (0.1.0 through 0.1.2) on the same day (September 6, 2020).

## Body
### Software Description
Geometricus is a software executable component classified as a "structure-based, alignment-free embedding approach for proteins." It generates embeddings—numerical representations—of proteins derived from their structural data. The "alignment-free" characteristic indicates that the software processes structural information without requiring a prerequisite step of aligning protein sequences, which can be computationally intensive or error-prone in traditional bioinformatics workflows.

### Development and Release History
The development of Geometricus has been tracked through several distinct versions hosted on GitHub.

*   **Initial Releases:** On September 6, 2020, three versions were released simultaneously or in quick succession: version 0.1.0, version 0.1.1, and version 0.1.2.
*   **Current Version:** The preferred and most recent version is **0.3.0**, published on April 20, 2022.

### Licensing and Repository
The project is maintained by the "TurtleTools" organization on GitHub.
*   **Repository URL:** `https://github.com/TurtleTools/geometricus`
*   **Homepage:** `https://turtletools.github.io/geometricus/`
*   **Legal:** The software operates under the **MIT License**, facilitating open collaboration and usage.

## References

1. [Source](https://api.github.com/repos/TurtleTools/geometricus)
2. [Release 0.1.0. 2020](https://github.com/TurtleTools/geometricus/releases/tag/v0.1.0)
3. [Release 0.1.1. 2020](https://github.com/TurtleTools/geometricus/releases/tag/v0.1.1)
4. [Release 0.1.2. 2020](https://github.com/TurtleTools/geometricus/releases/tag/v0.1.2)
5. [Release 0.3.0. 2022](https://github.com/TurtleTools/geometricus/releases/tag/v0.3.0)