Analyzing the aromatic-aromatic interactions in proteins: A2ID 2.0

The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (-) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619-networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (phi) were used to identify and characterize-networks. It was observed that among the 84,500 proteins with at least one aromatic-network, about 92.50 % of the instances are found to be either 2(77.34 %) or 3(15.23 %) networks. The analysis of interacting amino acid pairs in 2networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of-networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of-networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.