BioLiP2

BioLiP2 curates biologically relevant ligand–protein binding interactions from PDB entries and integrates functional annotations to support structure-based analyses.

Key Features:

• Primary data source: Primary structural data are sourced from the Protein Data Bank (PDB).
• Ligand relevance filtering: Application of geometric rules combined with experimental literature validations to identify biologically relevant ligands and distinguish them from purification and crystallization additives.
• Functional annotations: Integration of Enzyme Commission numbers, Gene Ontology terms, catalytic site annotations, and binding affinities from multiple databases and literature.
• Nucleic acid and large complexes: Expanded inclusion of nucleic acid–protein interactions and large complex interactions that were previously unavailable in PDB format.
• Structural search capabilities: Incorporation of structural alignment algorithms and structure prediction techniques enabling composite protein structure and sequence-based searching.
• Manual curation: Annotations are supplemented through a manual survey of the scientific literature.

Scientific Applications:

• Structural biology: Support for analysis of ligand–protein interactions and molecular mechanism studies using experimentally solved structures.
• Structure-based function annotation: Use of structure and sequence searches to infer protein function from ligand interactions.
• Docking and virtual screening: Supply of validated ligand–protein complexes for docking simulations and virtual ligand screening.
• Protein function analyses: Enabling detailed analyses of catalytic sites, binding affinities, and functional annotations for protein characterization.
• Therapeutic discovery: Provision of curated interaction data to aid development of novel therapeutic strategies.

Methodology:

Application of geometric rules, structural alignment algorithms, structure prediction techniques, and composite protein structure and sequence-based searching.