MycoWiki

MycoWiki provides a curated database of genes, proteins, structural data, and interaction networks for Mycoplasma pneumoniae, a minimal-genome (~700 protein-coding genes) organism, to support systems and synthetic biology research.

Key Features:

• Relational Database Structure: Data are organized within a relational database framework for structured storage and retrieval.
• Curated Gene and Protein Data: Comprehensive, manually curated annotations for Mycoplasma pneumoniae genes and proteins are maintained.
• Integration with AlphaFold Predictions: Structure predictions from the AlphaFold Protein Structure Database are incorporated for most proteins to aid functional interpretation.
• Structural Information from In Vivo Cross-linking: Structural data derived from in vivo cross-linking experiments are included to inform protein conformations and contacts.
• Protein-Protein Interaction Data: Results from global in vivo studies of protein-protein interactions are integrated to represent molecular interaction networks.

Scientific Applications:

• Systems Biology Analysis: Enables comprehensive analysis of cellular systems and network organization in Mycoplasma pneumoniae.
• Functional Annotation of Uncharacterized Proteins: Supports annotation efforts using structural predictions, cross-linking data, and interaction networks.
• Study of Minimal Cellular Life: Facilitates investigation of the minimal-genome biology and fundamental requirements for cellular viability.
• Synthetic Biology and Genome Engineering: Provides data resources relevant to engineering or modifying microbial systems based on Mycoplasma pneumoniae biology.

Methodology:

Curation of gene and protein annotations and integration of computational predictions (AlphaFold Protein Structure Database) with experimental datasets (in vivo cross-linking and global in vivo protein-protein interaction studies) within a relational database.