Dataset Information

INstruct: a database of high-quality 3D structurally resolved protein interactome networks.

ABSTRACT: INstruct is a database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction data with the specificity of atomic-resolution structural information derived from co-crystal evidence using a tested interaction interface inference method. Its web interface is designed to allow for flexible search based on standard and organism-specific protein and gene-naming conventions, visualization of protein architecture highlighting interaction interfaces and viewing and downloading custom 3D structurally resolved interactome datasets.INstruct is freely available on the web at http://instruct.yulab.org with all major browsers supported.

SUBMITTER: Meyer MJ

PROVIDER: S-EPMC3673217 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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INstruct: a database of high-quality 3D structurally resolved protein interactome networks.

Meyer Michael J MJ Das Jishnu J Wang Xiujuan X Yu Haiyuan H

Bioinformatics (Oxford, England) 20130418 12

<h4>Unlabelled</h4>INstruct is a database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction data with the specificity of atomic-resolution structural information derived from co-crystal evidence using a tested interaction interface inference method. Its web interface is designed to allow for flexible search based on standard and organism-specific protein and ge ...[more]

PMID: 23599502

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Project description: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.

Dataset Information

INstruct: a database of high-quality 3D structurally resolved protein interactome networks.

Publications

INstruct: a database of high-quality 3D structurally resolved protein interactome networks.

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