Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures

Area of Science:

• Biochemistry and Structural Biology
• Bioinformatics and Cheminformatics

Background:

• Binding MOAD (Mother of All Databases) is a long-standing repository of protein-ligand complexes and binding affinity data.
• The database has experienced substantial growth, currently housing 23,269 complexes and 8156 binding affinities.
• Annual updates involve semi-automated literature curation from PDB file references.

Purpose of the Study:

• To enhance the Binding MOAD platform for improved user experience and data accessibility.
• To introduce new functionalities for better visualization, searching, and data retrieval.
• To modernize the underlying technology stack for greater efficiency and scalability.

Main Methods:

• The Binding MOAD website was completely rewritten using the LAMP (Linux, Apache, MySQL, PHP) stack.
• New features include improved visualization plugins, advanced sorting and filtering, and filtered downloads.
• Structural queries based on ligands were introduced, alongside clustering of records by sequence identity to reduce redundancy.

Main Results:

• The upgraded platform offers an improved user interface with enhanced visualization tools.
• New search functionalities allow for field-based and ligand-based structural queries.
• Data redundancy is minimized through clustering based on 90% sequence identity.

Conclusions:

• The revamped Binding MOAD provides a more robust and user-friendly resource for accessing protein-ligand binding data.
• Enhanced features facilitate more efficient data exploration and analysis for researchers.
• The updated platform is better equipped to serve the scientific community's needs in studying molecular interactions.