D3PM: A Comprehensive Database for Protein Motions Ranging from Residue to Domain

Background: Knowledge of protein motions is significant to understand its functions. The currently available databases for protein motions, in general, are focused on overall domain motions, which pay little attention to local residue motions. Albeit with relatively small scale, the local residue motions may play crucial roles in protein functions and its binding with ligand, in particular for those residues within binding pockets. Results: A comprehensive protein motion database (D3PM) was constructed in this study to facilitate the analysis of protein motions. The D3PM has the motion information ranging from the overall structural changes of macromolecule to the local flip motion of the residues in ligand binding site. Currently, the D3PM has 5,339 entries of overall motions and 2,319 entries of pocket residues’ motions. The motion patterns in the database are classified into 4 types of overall structural change and 5 types of pocket residues’ shift. Impressively, it was found that less than 15% of the protein pairs have obvious overall conformational adaptations induced by ligand binding, while more than 50% of the protein pairs have significant structural changes in the ligand binding sites, indicating that ligand-induced conformational changes are drastic whereas they are mostly confined around the ligand. By the analysis of pocket residues’ preference, we classified amino acids into “pocketphilic” and “pocketphobic” residues, which is helpful to pocket prediction and ligand design.Conclusion: D3PM is a comprehenssive database about protein motions ranging from residue to domain, which should be useful for exploring diverse protein motions and for understanding protein functions. The database is freely available on www.d3pharma.com/D3PM/index.php.