NIMS: a database on nucleobase compounds and their interactions in macromolecular structures

Abstract

The intense exploration of nucleotide-binding protein structures has created a whirlwind in the field of structural biology and bioinformatics. This has led to the conception and birth of NIMS. This database is a collection of detailed data on the nucleobases, nucleosides and nucleotides, along with their analogues as well as the protein structures to which they bind. Interaction details such as the interacting residues and all associated values have been made available. As a pioneering step, the diffraction precision index for protein structures, the atomic uncertainty for each atom, and the computed errors on the interatomic distances and angles are available in the database. Apart from the above, provision has been made to visualize the three-dimensional structures of both ligands and protein–ligand structures and their interactions inJmolas well asJSmol. One of the salient features of NIMS is that it has been interfaced with a user-friendly and query-based efficient search engine. It was conceived and developed with the aim of serving a significant section of researchers working in the area of protein and nucleobase complexes. NIMS is freely available online at http://iris.physics.iisc.ernet.in/nims and it is hoped that it will prove to be an invaluable asset.