Registry Catalogue

HyPPI is a web-based tool for classifying protein–protein complexes as permanent, transient, or crystal artifacts. Permanent complexes are stable only in their associated state, whereas transient complexes can remain stable both as complexes and as individual subunits. Crystal artifacts are non-biological contacts formed during crystallization. HyPPI performs the classification using two structural properties of the protein–protein interface: its hydrophobicity (ΔG hydrophobic) and the interface quotient (IF-quotient), which reflects the symmetry of the interacting surfaces. Key benefits Automated classification of protein–protein complexes Distinguishes permanent and transient interactions from crystal artifacts Uses interpretable structural interface descriptors Supports assessment of the biological relevance of crystallographic contacts Web-based analysis without local software installation Applications Classification of protein–protein interactions in crystal structures Identification of potentially biologically relevant protein complexes Detection of non-functional crystallization contacts Analysis of interface hydrophobicity and symmetry Support for structural interpretation and protein interaction studies Intended use HyPPI is intended for structural biologists, protein scientists, bioinformaticians, and computational biologists working with three-dimensional protein complex structures. It is particularly useful for researchers who need to assess whether an observed protein–protein interface represents a permanent or transient biological interaction or is likely to be a crystal artifact.

JAMDA is a tool for preparing protein structures and docking small molecules into selected, preprocessed binding sites. It simplifies protein–ligand docking through automated workflows for protein preparation, binding-site setup, ligand conformer generation, docking, and scoring. Users can apply default settings or customize the preparation process to account for protein ensembles, relevant water molecules, and cofactors. Key benefits Automated preparation of proteins and binding sites Integrated docking and scoring of small-molecule ligands Flexible configuration for protein ensembles, water molecules, and cofactors Automated ligand conformer generation using Conformator Supports externally generated ligand conformations Designed for reproducible and streamlined docking workflows Applications Prediction of protein–ligand binding poses Virtual screening of small-molecule compounds Evaluation of alternative ligand conformations Docking into single structures or protein ensembles Investigation of the influence of binding-site waters and cofactors Support for structure-based drug discovery and ligand optimization Intended use JAMDA is intended for structural biologists, medicinal chemists, computational chemists, and researchers in structure-based drug discovery who need an automated and configurable workflow for protein–ligand docking. It is particularly suited for users who want to combine standardized preprocessing with flexible control over protein structures, binding-site components, and ligand conformations.

KIPEs (Knowledge-based Identification of Pathway Enzymes) is a web-based tool for the automated identification and functional annotation of enzymes involved in plant biosynthetic pathways. Using curated reference sequences, functionally relevant amino acid residues, and orthology-based inference, KIPEs identifies candidate genes in coding DNA (CDS), peptide, or transcriptome datasets and predicts their likely biological functions. The current release supports the annotation of enzymes involved in flavonoid biosynthesis (including decoration enzymes and transport proteins) as well as carotenoid biosynthesis. The tool is designed to facilitate the rapid characterization of metabolic pathways in newly sequenced plant species without requiring manual preparation of reference datasets. Key benefits Automated identification of pathway enzymes from CDS, peptide, or transcriptome data Functional annotation based on orthology and conserved functional residues Detection of functionally important amino acid motifs and catalytic sites No manual preparation of reference datasets required Fast and reproducible annotation workflow for newly sequenced species Produces annotated candidate sequences together with detailed summary reports Applications Annotation of enzymes involved in plant biosynthetic pathways Identification of candidate genes in genome and transcriptome assemblies Functional characterization of metabolic pathways Comparative genomics of biosynthetic gene families Evolutionary analysis of plant metabolism Candidate gene discovery for functional genomics and metabolic engineering Intended use KIPEs is intended for plant biologists, genome annotation specialists, bioinformaticians, and evolutionary researchers working with plant genome or transcriptome data. It is particularly suited for users seeking an automated and standardized workflow for the identification and functional annotation of enzymes involved in specialized plant metabolism.

LifeSoaks is a tool for identifying and characterizing solvent channels in macromolecular crystal structures determined by X-ray crystallography. It automatically evaluates channel accessibility by calculating bottleneck radii for solvent channels and small-molecule binding sites. By replacing time-consuming manual inspection, LifeSoaks supports the selection of suitable crystal forms and experimental conditions before soaking experiments. Key benefits Automated detection and analysis of solvent channels in crystal structures Calculation of bottleneck radii to estimate molecular accessibility Supports both solvent channel and small-molecule binding-site analysis Reduces the need for manual inspection of macromolecular crystal structures Rapid analysis, typically completed within seconds to minutes Helps prioritize promising crystal forms and soaking conditions Applications Planning of ligand- and fragment-soaking experiments Assessment of solvent channel accessibility in protein crystals Comparison of alternative crystal forms Identification of potential access routes to binding sites Selection and optimization of experimental soaking conditions Support for X-ray-based fragment screening Intended use LifeSoaks is intended for structural biologists, crystallographers, medicinal chemists, and researchers in structure-based drug discovery working with macromolecular crystal structures. It is particularly suited for users who want to assess whether small molecules can access binding sites before conducting soaking experiments.

LIFS (Lipidomics Informatics for Life Science) is a web portal providing a comprehensive suite of stand-alone and web-based tools for targeted and untargeted mass spectrometry-based lipidomics analysis. The platform supports lipid identification, quantification, quality control, visualization, and lipidome comparison, while also serving as an information hub for lipidomics resources, training, publications, and community activities. Key benefits Comprehensive ecosystem for lipidomics data analysis Combination of stand-alone software and web-based applications Supports both targeted and untargeted lipidomics workflows Standardized and reproducible analysis methods Interactive visualization and structure-based lipidome comparison Central hub for lipidomics software, courses, publications, and conferences Applications Lipid identification and annotation from mass spectrometry data Quantitative and qualitative lipidome comparison Quality control and post-processing of lipidomics datasets Generation of targeted transition lists for mass spectrometry workflows Parsing and normalization of lipid nomenclatures Statistical analysis and visualization of lipidomics experiments Included tools LipidXplorer – Shotgun lipidomics software using MFQL (Mass Spectrometry Formula Query Language) Lipidome Projector – Web application for structure-based lipidome comparison lxPostman – Post-processing and quality control for LipidXplorer outputs Goslin – Libraries and web tools for lipid nomenclature normalization LipidCreator – Creation of lipid-specific targeted transition lists LipidCompass – Interactive exploration and comparison of quantitative lipidomes LipidSpace – Interactive QC, lipidome comparison, statistical analysis, and visualization Intended use LIFS is intended for researchers in lipidomics, metabolomics, systems biology, and mass spectrometry-based life science research who require integrated tools for lipid identification, quantification, comparison, and visualization. The platform is particularly suited for users seeking standardized and reproducible lipidomics workflows supported by both web-based and stand-alone applications.

LipidCompass – Interactive Exploration and Comparison of Quantitative Lipidomes LipidCompass is a web-based database and analysis platform for the interactive exploration, comparison, and visualization of quantitative lipidomics datasets. It helps researchers navigate the lipid structural space and investigate lipid abundance patterns across samples, tissues, organisms, and studies. As part of the LIFS (Lipidomics Informatics for Life Science) ecosystem, LipidCompass serves as a FAIR resource for storing, exploring, and comparing lipidomics data using standardized nomenclature and metadata. Key benefits Interactive exploration of quantitative lipidomics datasets Comparison of lipidomes within and across studies FAIR data resource with standardized lipid annotations and metadata Integration with established lipid databases and controlled vocabularies Interactive visualization of lipid abundances and structural relationships Supports lipidomics data submitted in standardized formats such as mzTab-M Part of the broader LIFS lipidomics software ecosystem Applications Exploration and comparison of quantitative lipidomes Identification of similarities and differences between biological samples Cross-study comparison of lipidomics datasets Investigation of tissue-, organism-, and condition-specific lipid profiles Integration of lipidomics data into systems biology workflows Interactive visualization and interpretation of lipidomics experiments Intended use LipidCompass is intended for lipidomics researchers, mass spectrometry users, bioinformaticians, and systems biologists who need a centralized platform for exploring and comparing quantitative lipidomics data. It is particularly suited for users seeking FAIR-compliant data management, interactive visualization, and large-scale comparison of lipidomes across experiments and studies.

Lipidome Projector: Web-Based Application for Quantitative and Qualitative Lipidome Comparison Lipidome Projector is a web-based application designed to facilitate the comparison of lipidomes across different samples, conditions, or species. The tool enables researchers to visualize and analyze quantitative and qualitative differences in lipid profiles, providing insights into changes in lipid metabolism, regulation, and function. Key Features: Structure-based lipidome embeddings: Lipidome Projector uses a novel approach to embed lipid structures into a lower-dimensional space, allowing for the visualization of complex lipidomes. Quantitative and qualitative comparison: The tool enables researchers to compare lipid profiles both quantitatively (e.g., changes in lipid abundance) and qualitatively (e.g., changes in lipid structure). Interactive visualization: Lipidome Projector provides an interactive interface for exploring and visualizing lipidomes, allowing users to zoom in/out, rotate, and select specific lipids or groups of lipids. Benefits: Improved understanding of lipid metabolism: By comparing lipid profiles across different samples or conditions, researchers can gain insights into changes in lipid metabolism and regulation. Identification of biomarkers: Lipidome Projector can help identify potential biomarkers for diseases or disorders by highlighting changes in lipid profiles associated with specific conditions. Streamlined data analysis: The tool simplifies the process of comparing lipidomes, reducing the need for manual processing and allowing researchers to focus on interpreting results. Technical Details: Input data: Lipidome Projector accepts tables of lipid abundances and lipidome sample features in simple CSV formats. Output data: The tool generates interactive visualizations of lipidomes, which can be exported as images or used for further analysis. Collaboration: Lipidome Projector allows users to share their projects with colleagues or collaborators, facilitating collaborative research. Availability: Lipidome Projector is available as a web-based application on the LIFS Tools website. Users can access the tool by creating an account on the website.

LipidXplorer is a software tool designed for shotgun lipidomics, enabling researchers to identify and quantify lipids in complex biological samples. The software uses an language-driven approach for lipid identification expressed in MFQL (Mass Spectrometry Formula Query Language). Key Features: Shotgun lipidomics : LipidXplorer is specifically designed for shotgun lipidomics, allowing researchers to analyze complex lipid mixtures without the need for prior separation or fractionation. MFQL-based lipid identification : The software uses a language-driven approach for lipid identification, expressed in MFQL. This enables users to define specific queries for identifying lipids based on their molecular formulas and fragmentation patterns. High-performance analysis : LipidXplorer is designed for high-performance analysis, allowing researchers to process large datasets quickly and efficiently. Benefits: Improved accuracy and specificity : By using a language-driven approach for lipid identification, LipidXplorer enables researchers to improve the accuracy and specificity of their results. Increased sensitivity : The software's ability to analyze complex lipid mixtures without prior separation or fractionation enables researchers to detect lipids that may not be detectable by other methods. Streamlined workflow : LipidXplorer is designed to integrate with existing workflows, enabling researchers to quickly and easily incorporate shotgun lipidomics into their research. Technical Details: Input data : LipidXplorer accepts mass spectrometry data in various formats, including mzML and mzXML. Output data : The software generates output files that contain information on identified lipids, including molecular formulas, fragmentation patterns, and intensities. Operating system : LipidXplorer is available for Windows, macOS, and Linux operating systems. Availability: LipidXplorer is available as a free download from the LIFS Tools website. Users can access the software by creating an account on the website.

LPSN – List of Prokaryotic Names with Standing in Nomenclature LPSN (List of Prokaryotic Names with Standing in Nomenclature) is the authoritative online resource for the nomenclature of prokaryotes. Hosted by the DSMZ, it provides comprehensive and regularly updated information on validly published bacterial and archaeal names, their taxonomic status, nomenclatural history, and associated type strains. LPSN also integrates information from the Prokaryotic Nomenclature Up-to-date (PNU) service and links to type-strain genome data. Since 2023, LPSN has been recognized as a Global Core Biodata Resource. Key benefits Authoritative resource for prokaryotic nomenclature Regularly updated according to the latest taxonomic and nomenclatural changes Comprehensive information on validly published bacterial and archaeal names Links to type strains and associated genome information Integration of data from the Prokaryotic Nomenclature Up-to-date (PNU) service User-friendly web interface with powerful search capabilities Recognized as a Global Core Biodata Resource Applications Verification of valid bacterial and archaeal names Taxonomic classification and nomenclature research Identification of type strains and nomenclatural references Support for genome annotation and microbial database curation Comparative microbiology and microbial biodiversity studies Reference resource for publications and taxonomic assignments Intended use LPSN is intended for microbiologists, taxonomists, microbial ecologists, bioinformaticians, and life science researchers who require authoritative information on prokaryotic nomenclature and taxonomy. It is particularly suited for users involved in microbial classification, genome annotation, biodiversity research, and the curation of microbial databases.

lxPostman is a web-based application designed to facilitate the post-processing of output files generated by LipidXplorer, a software tool for shotgun lipidomics. The application provides a user-friendly interface for quality control, quantitation, and merging of results from multiple runs or samples. Key Features: Quality control : lxPostman allows users to evaluate the quality of their data by assessing metrics such as signal-to-noise ratio, peak intensity, and retention time. Quantitation : The application enables users to quantify lipids based on peak areas, heights, or intensities, and to normalize results using various methods (e.g., TIC normalization). Merging results : lxPostman allows users to combine results from multiple runs or samples, creating a single output file that contains all the data. Interactive visualization : The application provides an interactive interface for visualizing lipid profiles, allowing users to explore and compare results in detail. Benefits: Improved data quality : By providing tools for quality control and quantitation, lxPostman helps ensure that lipidomics data is accurate and reliable. Increased efficiency : The application streamlines the process of post-processing LipidXplorer output files, saving time and reducing manual effort. Enhanced collaboration : lxPostman allows users to share their results with colleagues or collaborators, facilitating collaborative research. Technical Details: Input data : lxPostman accepts output files generated by LipidXplorer in various formats (e.g., CSV, Excel). Output data : The application generates output files that contain quality-controlled and quantified lipidomics data, which can be used for further analysis or exported to other software tools. Integration with LipidXplorer : lxPostman is designed to work seamlessly with LipidXplorer, allowing users to easily transfer results between the two applications. Availability: lxPostman is available as a web-based application on the LIFS Tools website. Users can access the tool by creating an account on the website.

MacPepDB is a database that enables fast and comprehensive access to all theoretically generated tryptic peptides derived from the UniProtKB. It allows users to query peptide sequences across organisms and proteomes, facilitating proteomics research that relies on in silico digestion and peptide-centric analyses. Key benefits Fast retrieval of tryptic peptides derived from UniProtKB proteins Organism- and proteome-wide peptide search capabilities Supports peptide-centric workflows in proteomics research Facilitates theoretical digestion-based analyses Web-accessible database for immediate querying Applications In silico tryptic digestion of UniProtKB protein entries Peptide lookup across species and proteomes Support for mass spectrometry-based proteomics workflows Assessment of peptide uniqueness and proteome coverage Database support for method development and benchmarking Intended use MacPepDB is intended for researchers in proteomics, bioinformatics, and computational biology who require rapid access to theoretical tryptic peptides for database searches, method development, or peptide-centric analyses. It is particularly suited for users working with mass spectrometry data and proteome-wide peptide investigations.

MapMan is a desktop tool for visualizing plant high-throughput omics data in the context of biological pathways and processes. It maps protein function annotation results, generated with Mercator4, together with gene expression data onto schematic pathway diagrams. This visual approach enables researchers to inspect global biological responses and identify altered biological processes within their experiments. Key benefits Desktop application for Windows, macOS, and Linux Visualization of gene expression data together with protein function annotations Mapping of experimental data onto schematic pathway and process diagrams Compatible with current and legacy Mercator4 annotation outputs Supports custom diagrams using pathway images and protein/gene mapping files Applications Visualization of plant gene expression data in biological context Exploration of metabolic pathways and other biological processes Inspection of global response patterns across experiments Use of predefined MapMan diagrams, including Mercator4-compatible diagram sets Creation of custom pathway diagrams for project-specific analyses Intended use MapMan is intended for plant scientists, molecular biologists, bioinformaticians, and omics researchers working with plant gene expression data and protein function annotations. It is particularly suited for users who want to visually explore large datasets using pathway-based diagrams and Mercator4-compatible classification outputs.