# Atom3D

> a unified collection of datasets and machine learning tools concerning the three-dimensional structure of biomolecules, including proteins, small molecules, and nucleic acids

**Wikidata**: [Q114878673](https://www.wikidata.org/wiki/Q114878673)  
**Source**: https://4ort.xyz/entity/atom3d

## Summary
Atom3D is a unified collection of datasets and machine learning tools focused on the three-dimensional structure of biomolecules, including proteins, small molecules, and nucleic acids. It serves as an open-source software resource for biological data, providing a standardized platform for computational analysis.

## Key Facts
- **Definition:** A unified collection of datasets and machine learning tools concerning the 3D structure of biomolecules.
- **Scope:** Encompasses proteins, small molecules, and nucleic acids.
- **License:** Released under the MIT License.
- **Category:** Classified as open-source software and biological data.
- **Website:** https://www.atom3d.ai/
- **Source Repository:** Hosted at https://github.com/drorlab/atom3d.
- **ArXiv ID:** Associated with the identifier 2012.04035.
- **Latest Version:** Version 0.2.6 (released July 20, 2022).
- **Initial Release:** Version 0.1.0 (released January 2, 2021).

## FAQs
### Q: What types of biomolecules are included in Atom3D?
Atom3D covers a range of biomolecular structures, specifically including proteins, small molecules, and nucleic acids.

### Q: What license is Atom3D released under?
The software is released under the MIT License, which permits users to use and redistribute the code.

### Q: What is the most recent version of Atom3D?
The most recent version is 0.2.6, which was published on July 20, 2022.

### Q: Where can Atom3D be accessed?
The project's source code is available on GitHub at `https://github.com/drorlab/atom3d`, and additional information can be found on its official website at `https://www.atom3d.ai/`.

## Why It Matters
Atom3D addresses a critical need in computational biology for standardized, machine-learning-ready datasets focused on 3D biomolecular structure. By unifying data on proteins, small molecules, and nucleic acids with specific machine learning tools, it lowers the barrier to entry for researchers developing algorithms for structural biology. The project's open-source nature under the MIT License fosters reproducibility and collaboration, allowing the scientific community to build upon a shared foundation rather than fragmenting efforts across incompatible data formats.

## Notable For
- **Unified Data Collection:** It distinguishes itself by integrating datasets across multiple biomolecular domains—proteins, small molecules, and nucleic acids—into a single unified collection.
- **Machine Learning Focus:** It is specifically designed to support machine learning applications, providing not just data but also the tools necessary for analysis.
- **Active Development History:** The project demonstrated active development throughout 2021 and 2022, releasing 16 distinct versions between January 2021 and July 2022.

## Body
### ### Project Definition and Scope
Atom3D is defined as a unified collection of datasets and machine learning tools. Its primary subject matter is the three-dimensional structure of biomolecules. The scope of the data includes three main categories: proteins, small molecules, and nucleic acids. It is classified as a type of biological data and open-source software.

### ### Development and Release History
The development of Atom3D is documented through a series of software releases beginning in early 2021. The initial release, version 0.1.0, was published on January 2, 2021. This was quickly followed by versions 0.1.1 and 0.1.2 on the same day. Subsequent updates occurred throughout early 2021, including versions 0.1.3 (February 2, 2021), 0.1.4 (February 3, 2021), 0.1.5 (February 3, 2021), 0.1.6 (February 4, 2021), and 0.1.7 (February 12, 2021).

Major version increments continued with version 0.2.0 on February 23, 2021, followed by maintenance releases: 0.2.1 (March 15, 2021), 0.2.2 (April 16, 2021), 0.2.3 (June 22, 2021), and 0.2.4 (June 27, 2021). After a hiatus, development resumed in 2022 with version 0.2.5 on July 19, 2022, and the final recorded version, 0.2.6, on July 20, 2022.

### ### Technical Specifications and Access
The project is accessible via its website at `https://www.atom3d.ai/` and its source code repository located at `https://github.com/drorlab/atom3d`. The software utilizes the MIT License, a permissive free software license. The project is associated with an academic paper tracked under the arXiv ID 2012.04035.

### ### Relationship to Open-Source Software
As an instance of open-source software, Atom3D inherits the characteristics of this software class. Open-source software is defined by a permissive license that grants libre access to the original source code, allowing users to use and redistribute the software in its current state. This classification positions Atom3D within the broader ecosystem of open knowledge and source-available software, contrasting it with proprietary software models.

## References

1. [Source](https://api.github.com/repos/drorlab/atom3d)
2. [Release 0.1.0. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.0)
3. [Release 0.1.1. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.1)
4. [Release 0.1.2. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.2)
5. [Release 0.1.3. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.3)
6. [Release 0.1.4. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.4)
7. [Release 0.1.5. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.5)
8. [Release 0.1.6. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.6)
9. [Release 0.1.7. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.1.7)
10. [Release 0.2.0. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.2.0)
11. [Release 0.2.1. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.2.1)
12. [Release 0.2.2. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.2.2)
13. [Release 0.2.3. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.2.3)
14. [Release 0.2.4. 2021](https://github.com/drorlab/atom3d/releases/tag/v0.2.4)
15. [Release 0.2.5. 2022](https://github.com/drorlab/atom3d/releases/tag/v0.2.5)
16. [Release 0.2.6. 2022](https://github.com/drorlab/atom3d/releases/tag/v0.2.6)