Services: Proteins And Proteomes

Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

A database of structural features for three galactose metabolism enzymes (GALT, GALK, GALE).

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

GeoMine enables textual, numerical and 3D searching with full chemical awareness in binding sites of the entire PDB dataset. 

Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.

GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carry them, the enzymes that synthesise or degrade them and the proteins that bind them.

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

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. 

Estimation of transmembrane regions based on amino acid sequence

Web server for identification of hot spots in protein engineering.

Human transmembrane proteome database

Database with millions of high-resolution images.

HyPPI classifies a protein-protein complex concerning its interaction type into a permanent, transient or crystal artifact. 

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

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.

A web service for the structural annotation of protein-protein interaction networks. 

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.

JAMDA docks small molecules into protein binding sites.

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

LifeSoaks calculates solvent channels and their corresponding bottleneck radii by constructing a three dimensional Voronoi diagram. 

The Medical Proteome Center at Ruhr-University Bochum offer consulting and analysis services to support users in bioinformatics and statistical analysis of proteomics data and associated clinical data.