Services: Molecular And Cellular Structures

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

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. 

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.

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).

Predicts the subcellular localization of proteins in eukaryotes.

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

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

A classification of protein structures and sequences that groups protein domains into superfamilies. 

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.

CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases.

A server for calculating contact maps of X-ray, NMR and predicted structures.

System for identification of alterations using protein mass spectrometry.

A manually curated community resource annotating proteins for experimentally determined regions of intrinsic disorder from the literature.

Web interface for assignment and analysis of DNA conformers.

Database Of Local Biomolecumal COnfromers. (Formerly known as DOLCE)

This resource includes sequence pipeline (TarO) analysis, a secondary prediction (JPred) structure server, and a protein kinase database and kinase classification pipeline (Kinomer).

R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images. In the context of high-throughput microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. Part of the Human Omics Analysis Toolbox

Easily interpretable electron density score for individual atoms. 

The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

A Python framework for the analysis and visualization of trees.

FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools.

An online access to a series of RNA research tools for sequence-structure alignments, clustering, interaction prediction, identification of homologs etc

A specialized and medically-oriented database of published variations observed within the internal ribosome entry site (IRES) variants in hepatitis C virus.

Web server for identification of hot spots in protein engineering.

Human transmembrane proteome database

Database with millions of high-resolution images.