ribosome.xyz

What It Is

RiboXYZ (ribosome.xyz) is an interactive database and API service focused on atomic structures of ribosomes. Developed by Artem Kushner, Khanh Dao Duc, and others, the project has been published in Nucleic Acids Research. It provides structural biology researchers with a standardized interface for programmatic access to ribosome structures and ligand-binding site data.

Core Dimensions

• Features and Use Cases: RiboXYZ has two main functions. First, structural search: it can retrieve IDs and full metadata for all ribosome structures in the PDB, with advanced filtering by year, polymer class (such as tRNA), and subunit completeness (SSU+LSU). Second, ligand-binding site analysis: it can query residues surrounding non-polymeric ligands (such as antibiotics) in a specific structure, and can also predict potential binding pockets for a ligand on a target ribosome structure based on binding sites observed in known structures.
• API/SDK: The tool is delivered entirely through a RESTful API, supports standard GET and POST requests, and returns data in JSON format. The material provides detailed cURL examples covering the full workflow, from basic ID retrieval and metadata queries to binding-site prediction, making it highly developer-friendly.
• Integrations and Ecosystem: It is deeply integrated with the PDB (Protein Data Bank), and its structure IDs, such as 4UG0 and 7K00, directly correspond to PDB standards.
• Open Source and Self-Hosting: The text only mentions that the project is supported by open-source institutions. It does not clearly state whether RiboXYZ itself is open source, nor does it provide any self-hosting option.
• Documentation Quality: Based on the examples provided, the API endpoints appear well designed, with clear parameters such as radius and chemical ID, offering a solid developer experience. However, the overall documentation quality would need to be assessed against the full API documentation site.

Pricing

As an academic research project, the text does not mention any paid plans or fees. The API can be accessed directly via cURL, so it is presumably free and publicly available.

Pros and Cons

Pros: Extremely specialized in its domain, filling a gap for dedicated ribosome structure search; RESTful API design; ligand-binding site prediction is highly valuable for research; strong academic credibility. Cons: Very narrow audience, useful mainly to structural biology and computational chemistry researchers; limited information about a frontend UI or interactive interface; no clearly stated service availability guarantee or SLA.

Who It’s For

Designed for structural biologists, computational chemists, bioinformatics developers, and researchers studying interactions between antibiotics and ribosomes, such as the E. coli ribosome.

Access from China and Alternatives

Access from China: Unknown. As an academic .xyz domain, it is unlikely to face commercial blocking, but actual network connectivity should be tested. Payment: Free, no payment required. Alternatives: The official RCSB PDB database, though it lacks RiboXYZ’s ribosome-specific advanced filtering and ligand-prediction API.