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A method and server for predicting damaging missense mutations
TLDR
A new method and the corresponding software tool, PolyPhen-2, which is different from the early tool polyPhen1 in the set of predictive features, alignment pipeline, and the method of classification is presented and performance, as presented by its receiver operating characteristic curves, was consistently superior. Expand
STRING v10: protein–protein interaction networks, integrated over the tree of life
TLDR
H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database. Expand
A human gut microbial gene catalogue established by metagenomic sequencing
TLDR
The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species. Expand
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
TLDR
An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Expand
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
TLDR
The update to version 9.1 of STRING is described, introducing several improvements, including extending the automated mining of scientific texts for interaction information, to now also include full-text articles, and providing users with statistical information on any functional enrichment observed in their networks. Expand
Functional organization of the yeast proteome by systematic analysis of protein complexes
TLDR
The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery. Expand
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
TLDR
The latest version of STRING more than doubles the number of organisms it covers, and offers an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. Expand
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
TLDR
In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Expand
STRING 8—a global view on proteins and their functional interactions in 630 organisms
TLDR
The most important new developments in STRING 8 over previous releases include a URL-based programming interface, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures. Expand
SMART, a simple modular architecture research tool: identification of signaling domains.
TLDR
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool that allows rapid identification and annotation of signaling domain sequences, showing that at least 6.7% of yeast genes contain one or more signaling domains, approximately 350 greater than previously annotated. Expand
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