Service list

A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members.

A collection of high-resolution three-dimensional structural templates for domain-domain interactions. It contains templates for interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab.

A reusable platform-independent API call component for protein metadata alignment, annotation, and integration across major protein data resources.

CSC develops and hosts an open source tool REMS to assist a DAC to manage Data Access Applications and access rights to sensitive datasets. REMS is a key component in ELIXIR AAI.

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis.

ActivityFinder establishes a connection between crystallographic data stored in the PDB database and the activity values stored in the ChEMBL database.

APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). 

The AgroLD (Agronomy Linked Data) Knowledge Graph is a specialized RDF database that integrates genomic and genetic information in plant science.

Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting and flexible feature annotation.

This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file).

A Consensus Method for Amyloid Propensity Prediction

ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository.

http://motherbox.chemeng.ntua.gr/anastasia_dev/

ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Web portal for the annotation of pathological protein variants.

APICURON is a database to credit and acknowledge the work of biocurators. It collects and aggregates biocuration events from third party resources generating achievements and leaderboards.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. 

A customised Galaxy instance for the genomic characterisation of microoganisms in particular and data intensive biomedical research in general.

Aruna Object Storage is a data lake storage system that manages scientific data and a rich set of associated metadata according to FAIR principles.

Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts

ASAP (Automated Single-cell Analysis Portal) is a web-based, collaborative portal aimed at democratizing single-cell omics data analyses and to render it more accessible to researchers. ASAP does not require any installation and enables standardized analyses that can be run in minutes by any user without requiring significant computing power. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools, and guiding them through tutorials.

Alternative splicing database of human genes and functional annotation of their isoforms using the ASPic algorithm.

Atomic Charge Calculator - web application using the Electronegativity Equalization Method.

AuReMe, is an adaptable workspace for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. It is adapted to the metabolic study of non-conventional organisms and microbiomes to ensure that the process is reproducible and documented regardless of the combination of tools used. Among others, modules included in the AuReMe environment are a model-management PADmet module, a wiki-export module, a gap-filling tool for non-conventional organism (meneco), a tool for the reduction of microbial communities based on metabolic complementarities (miscoto) and a package to handle the analysis of large-scale microbiota (Metage2Metabo).

The ELIXIR AAI (Authentication and Authorisation Infrastructure) is the ELIXIR service portfolio for authenticating users and helping relying services to manage users' access rights in the services. 

BacDive represents a collection of organism-linked information covering the multifarious aspects of bacterial and archaeal biodiversity. The content encloses information on taxonomy, morphology, physiology, sampling and environmental conditions as well as molecular biology.

Predicts the subcellular localization of proteins in eukaryotes.

Bakta is a tool for the rapid and standardised annotation of bacterial genomes and plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON and bioinformatics standard file formats for automatic downstream analysis.

Benchmark Energy and geometry DataBase is available through web interface with integrated analytical tools.