| URL: | https://acds.neist.res.in/cadv2 |
| Full name: | Cation-Aromatic Database |
| Description: | CAD 2.0 contains information on approximately 27.26 million cation-aromatic motifs, classifying them as cation-π or cation-σ motifs and analyzing their occurrence in various protein classes. The database aids in identifying cation-π interactions and developing new methods and force fields. |
| Year founded: | 2007 |
| Last update: | 2024-06-30 |
| Version: | v2.0 |
| Accessibility: |
Accessible
|
| Country/Region: | India |
| Data type: | |
| Data object: |
NA
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| Database category: | |
| Major species: |
NA
|
| Keywords: |
| University/Institution: | Indian Institute of Chemical Technology |
| Address: | Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India |
| City: | |
| Province/State: | Assam |
| Country/Region: | India |
| Contact name (PI/Team): | G. Narahari Sastry |
| Contact email (PI/Helpdesk): | gnsastry@iict.res.in |
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Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0. [PMID: 37789571]
The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2. |
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Cation-aromatic database. [PMID: 17377989]
Cation-aromatic database (CAD) is a publicly available web-based database that aims to provide further understanding of interaction between a cation and the pi interactions. A tool to identify the interactions in a user-given protein is also added to the database. CAD is freely accessible via the Internet at http://203.199.182.73/gnsmmg/databases/cad/. |