Services: proteins and proteomes

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

HAMAP is a system for the classification and functional annotation of protein sequences. It consists of a collection of expert curated family profiles for protein classification and associated rules for protein annotation. 

Web server for identification of hot spots in protein engineering.

Database with millions of high-resolution images.

Predicts protein stability changes upon single point mutation from protein structure or protein sequence.

ionomicHUB provides curated ionomic data on many thousands of plant samples freely available to the public. It is an international collaborative cyber research environment to help identify and understand the genes and gene networks that function to control the ionome, the mineral nutrient and trace element composition of an organism or tissue. 

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

Interaction Network GO Annotator is a web server for the prediction of protein function.

Prediction of protein stability change upon single-point variations from protein sequence and structure

IntAct provides a freely available, open source database system and analysis tools for molecular interaction data.

IntEnz is a database of enzyme nomenclature that also provides enzyme classifications based on the nature of catalysed reactions. IntEnz is produced in collaboration with the SIB Swiss Institute of Bioinformatics.

InterPro classifies proteins into families and predicts the presence of important domains and sites.

iPath is a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. Users can map their own data onto these pathway maps. Due to its navigation and customization functions, iPATH thus allows users to easily explore and analyze the functional and metabolic capabilities of their (meta-)genomic data sets. Part of the Microbiome Analysis Toolbox. 

Integrated Proteogenomics DataBases an open source database that provides integrated annotations, predictions and a six-frame translation for one respective genome sequence in an easily usable format, both as a search DB (FASTA format) with informative identifiers and a GFF file that integrates all annotations and identifiers.

Consolidated resource of public binary protein-protein interaction data assembled from more than 15 individual binary protein-protein interactions datasets

An open access database of manually curated, non-redundant transcription factor (TF) binding profiles

KEGGanim is a tool for visualizing data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying high-throughput data over handdrawn KEGG pathway maps.

Access to aRNA research tools for secondary structure prediction, structure alignments, interaction prediction, kinetics etc. Databases and Utils include:

• TRNAdb
• Mitos
• DARIO
• Plexy
• RNAsnoop
• RNAstrand 
• Ryoto

A comprehensive collection of data from manually curated protein-protein interaction databases adhering to the IMEx consortium.

A software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference

The Molecular INTeraction Database of protein-protein interactions curated from peer-reviewed papers. An ELIXIR Core Data Resources and founder member of the IMEx Consortium.

The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates. Missense3D predicts the structural changes introduced by an amino acid substitution.

A database of protein disorder and mobility annotations, designed centralize resources for annotations of intrinsic protein disorder and its function. Part of the InterPro consortium, an ELIXIR Core Data Resource.

The archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB- Dev for integrative structures. Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive. This includes single chains or complexes consisting of proteins, RNA, DNA, or carbohydrates including small molecules bound to them.

Tool to predict peptide fragment ion intensities for mass spectrometry-based proteomics data.

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

An innovative knowledge platform dedicated to human proteins. It contains a wealth of data on all the human proteins that are produced by the 20'000 protein- coding genes found in the human genome. 

Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity.

(Oligogenic Resource for Variant Analysis) is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes).

Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences;