A new bioinformatics analysis tools framework at EMBL-EBI.

The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes.

Fast and efficient searching of biological data resources--using EB-eye.

The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property.

Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms.

Analyzing protein-protein interactions at the atomic level is critical for our understanding of the principles governing the interactions involved in protein-protein recognition. For this purpose, descriptors explaining the nature of different protein-protein complexes are desirable. In this work, the authors introduced Epic Protein Interface Classification as a framework handling the preparation, processing, and analysis of protein-protein complexes for classification with machine learning algorithms.