Services: Molecular and cellular structures
Name of service | Tag | Related links* | Key collection | |
---|---|---|---|---|
3DBIONOTES API |
A reusable platform-independent API call component for protein metadata alignment, annotation, and integration across major protein data resources. |
bio.tools | RIR | |
Atomic Charge Calculator |
Atomic Charge Calculator - web application using the Electronegativity Equalization Method. |
bio.tools | ||
BaCelLo |
Predicts the subcellular localization of proteins in eukaryotes. |
bio.tools | ||
BEGDB |
Benchmark Energy and geometry DataBase is available through web interface with integrated analytical tools. |
bio.toolsFAIRsharing | ||
BioXSD / GTrack |
The BioXSD / GTrack ecosystem is an infrastructure of generic state-of-the-art data formats for integrative bioinformatics, with focus on genomics and epigenomics, sequence and structure bioinformatics, and other applications. |
|||
CAMEO |
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. |
bio.toolsFAIRsharing | ||
CATH/Gene3D |
A classification of protein structures and sequences that groups protein domains into superfamilies. |
bio.toolsFAIRsharingTeSS | CDR | |
CAVER 3.0 |
Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures. |
bio.tools | ||
CoCoMaps |
A server for calculating contact maps of X-ray, NMR and predicted structures. |
bio.tools | ||
CRISPRdb |
The CRISPRdb database and services are leading international resources for CRISPR sequence analysis. |
bio.toolsFAIRsharing | ||
Decryptor |
System for identification of alterations using protein mass spectrometry. |
bio.tools | ||
DisProt |
A manually curated community resource annotating proteins for experimentally determined regions of intrinsic disorder from the literature. |
bio.toolsFAIRsharing | ||
DNATCO |
Web interface for assignment and analysis of DNA conformers. |
bio.tools | ||
Dolbico (formely DOLCE) |
Database Of Local Biomolecumal COnfromers. |
bio.toolsFAIRsharing | ||
EMDB |
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. |
bio.toolsFAIRsharing | EDD | |
Expression atlases |
These include the Human Developmental Studies Network (HuDSeN), emouseatlas.org, echickatlas.org, and macrophages.com, a gene expression atlas of the domestic pig. |
|||
HotSpot Wizard |
Web server for identification of hot spots in protein engineering. |
bio.tools | ||
Human Protein Atlas (HPA) |
Database with millions of high-resolution images. |
bio.toolsFAIRsharing | CDR | |
I-Mutant 2.0 |
Predicts protein stability changes upon single point mutation from protein structure or protein sequence. |
bio.tools | ||
InterPro |
InterPro classifies proteins into families and predicts the presence of important domains and sites. |
bio.toolsFAIRsharingTeSS | CDR | |
IreSite |
Non-coding genome sequences and genetic network tools. The IRESite presents experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. |
bio.toolsFAIRsharing | ||
MobiDB |
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. |
bio.toolsFAIRsharing | ||
MOLE |
Toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures, e.g., proteins, RNA, DNA and biomacromolecular assemblies. |
bio.tools | ||
MOLEonline |
Web interface providing a direct access to MOLE 2.0 functionality and enabling on-line and easy-to-use interactive channel analysis. |
bio.tools | ||
MotiveValidator |
Web based application to validate ligand structure in PDB. |
bio.tools | ||
Pasta |
Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences; |
|||
PatternQuery/PatternExplorer |
Software to identify defined fragments in biomacromolecules. |
bio.tools | ||
Pfam |
Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). |
bio.toolsFAIRsharing | ||
PhD-SNP |
Predictor of human deleterious Single Nucleotide Polymorphisms. |
bio.tools | ||
Phyre2 |
A suite of tools available on the web to predict and analyze protein structure, function and mutations. |
bio.tools |