Services: proteins and proteomes

A platform for interpretation of proteomics identification results from multiple search engines.

Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). 

Predictor of human deleterious Single Nucleotide Polymorphisms.

A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source information and enables primary PPI dataset cross-checking. The PICKLE web-based interface allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein or the gene level, at three PPI filtering modes.

A dedicated web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method

An open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables.

The Protein Model Database stores manually built 3D models of proteins.

A prediction system for GPI-anchored proteins.

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. 

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

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.

Webtool for automated quality control and statistical analysis of protein expression following labelled mass spectrometry experiments

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.

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.

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. 

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.