Services: Proteins And Proteomes

PRIDE (The Proteomics Identifications Database) is a standards-compliant, public repository for proteomics data. It contains protein and peptide identifications and their associated supporting evidence.

Tool for the detection of structurally similar protein binding sites and pairwise local structural alignment

PROSITE consists of entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. PROSITE is a key element of the UniProt annotation pipeline “UniRule”. 

A complete, flexible analysis of protein microarrays for biomarker discovery. Part of the Proteomics Toolbox. 

The Protein Data Bank in Europe (PDBe) is the European part of the wwPDB for the collection, organisation and dissemination of data on biological macromolecular structures.

An algorithm suite combining Protein Spectrum Matches from different experiments / search engines for consistent, comparable results. Part of the Proteomics Toolbox. 

 ProteinsPlus support life scientists in working with protein structures, and focuses on protein-ligand interactions. The server provides support for the initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. 

ProteoSign: an end-user online differential proteomics statistical analysis platform

Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. 

A software tool for the identification of common transcription factors that are likely to regulate a user defined set of genes. PscanChIP is the extension of Pscan to process ChIP-Seq enriched regions.

The PSIPRED Protein Structure Analysis Workbench aggregates several UCL Bioinformatics Group prediction methods into one location. 

A PyMOL plugin, designed to act as simple and intuitive interface between PyMOL and several bioinformatics tools.

A database of annotated tandem repeat protein structures, combining computer-based methods and manual curation.

Residue interaction network generator. RING identifies all types of non-covalent interactions at atomic level in a protein structure (PDB);

A comprehensive data resource for salmonids species based on different omics data

A database with high-quality curated and freely accessible SARS-CoV-2 genomics- and contextual resources.

Comprehensive resource of human phosphosites within their full context.

SIENA has been developed for the automated assembly and preprocessing of protein binding site ensembles.

The SIGnaling Network Open Resource annotates signaling information from the literature as binary causative relationships.

Web application to compare multiple protein structural motifs.

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms. Part of the Human Omics Analysis Toolbox. 

Prediction of single point protein mutations likely to be involved in disease.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. 

StructureProfiler is a tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods.

SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals.

Database of protein expression time series for specific experiments on streptomyces, caulobacter, neiseria.

SWISS-MODEL Repository is a continuously updated database of annotated protein structure homology models generated by the fully automated SWISS-MODEL modelling pipeline. 

SWISS-MODEL is a fully automated service for protein structure homology modelling. It provides a personal web based workspace for interactive modelling, storing project data and visualizing results online. 

SwissBioPics is a freely available library of interactive biological images for visualizing subcellular location data. It includes cell types from all kingdoms of life - from muscle, neuronal and epithelial cells of animals to rods, cocci, clubs, spirals, and other more exotic forms of bacteria and archaea.