D3PM

D3PM catalogs protein domain and ligand-binding pocket motions to provide a repository of global domain movements and local residue shifts relevant to ligand binding.

Key Features:

• Comprehensive Motion Data: Contains 5,339 entries of overall protein motions and 2,319 entries of local residue movements within ligand-binding pockets.
• Classification of Motions: Categorizes motion patterns into four distinct types of overall structural changes and five types of pocket residue shifts.
• Focus on Ligand-Induced Changes: Reports that less than 15% of protein pairs exhibit significant global conformational changes upon ligand binding while over 50% show substantial structural changes localized to ligand-binding sites.
• Amino Acid Classification: Introduces a classification of amino acids in binding pockets as "pocketphilic" or "pocketphobic" based on their behavior in pockets.

Scientific Applications:

• Protein Function Exploration: Enables analysis of how global and local motions relate to protein biological function.
• Ligand Design and Drug Discovery: Informs ligand design by detailing pocket-specific residue movements and binding-site variability.
• Structural Biology Research: Supports study of conformational changes and stability through curated domain- and residue-level motion data.

Methodology:

D3PM was constructed by systematically compiling motion data from multiple sources and organizing entries using defined classification criteria for overall structural changes and pocket residue shifts.