Abstract
Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface.Database URL: http://dommino.org
Highlights
Interactions between three major types of macromolecules in a cell, proteins, DNAs and RNAs, underlie the cell’s basic functioning and are implicated in many diseases [1,2,3,4,5]
We have found that a number of structural classification of proteins (SCOP) domains cannot be correctly located in the current versions of some Protein Data Bank (PDB) entries, and we can use only 107 360 SCOP domains from 37 439 PDB entries
The newly designed database of structurally resolved macromolecular interactions, DOMMINO 2.0, contains comprehensive information about the interactions mediated by all three major classes of biomolecules in a living organism: proteins, RNAs and DNAs
Summary
Interactions between three major types of macromolecules in a cell, proteins, DNAs and RNAs, underlie the cell’s basic functioning and are implicated in many diseases [1,2,3,4,5]. These diverse molecular interactions constitute the basic building blocks of a complex macromolecular assembly [6,7,8]. Databases on RNA- and DNA-mediated interactions occur in much smaller numbers and include BIPA [29], NDB [30], NPIDB [31] and PRIDB [32].
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