Seamless Access to Open Cheminformatics with New Web Interface

We are excited to announce the release of Cheminformatics Microservice 3.1.0, featuring a new web application interface that makes cheminformatics tools accessible to everyone – no coding required!
This release represents a significant step forward in making cheminformatics tools more accessible to the broader scientific community, furthering the mission of open science and collaborative research in chemistry and related fields. 

Bridging the Gap Between Tools and Users

Cheminformatics Microservice has established itself as a comprehensive open-source solution that provides unified access to multiple cheminformatics toolkits (RDKit, Chemistry Development Kit, and OpenBabel) through a standardised REST API. With this new release, we’ve significantly expanded accessibility by introducing a user-friendly web interface available at app.naturalproducts.net.

The platform eliminates the overhead of installing and maintaining complex cheminformatics tools individually, serving as an ideal solution for researchers, educators, students, and industry professionals who need quick access to chemical analysis functions.

We invite you to explore the platform and experience how it can enhance your cheminformatics workflows!

New Web Application

The newly launched web application is available at app.naturalproducts.net and transforms how users interact with cheminformatics tools through an intuitive, modern interface. Key features include:

  • Interactive Chemical Visualization: View molecular structures in both 2D and 3D with customizable rendering options
  • Structure Drawing Interface: Create and edit molecules using the integrated Ketcher editor
  • PubChem Integration: Directly fetch compounds by name, SMILES, InChI, CAS number, or formula
  • Structure Generation: Generate chemical structures based on molecular formulas
  • Image-to-Structure: Extract chemical structures from images using DECIMER (optical chemical structure recognition)
  • Comprehensive Property Calculation: Generate molecular descriptors and analyze structures
  • Sugar Moiety Analysis: Detect and remove sugar moieties from complex structures
  • Chemical Filtering System: Screen compounds using PAINS, QED, Lipinski, Ghose, Veber, and Rule of Three
  • Format Conversion Hub: Seamlessly convert between SMILES, InChI, InChIKey, SELFIES, and other formats

Enhanced InChI Integration

A standout feature of this release is the comprehensive InChI integration, similar to the InChI web demo provided by the InChI Trust, providing researchers with essential tools for maintaining chemical identity standards:

  • Interactive InChI Converter: Draw structures and instantly generate corresponding InChI strings
  • RInChI Support: Represent chemical reactions with standardised RInChI notation
  • Advanced Configuration Options: Customize InChI parameters for stereochemistry, isotopic information, and more

Advanced Capabilities Under the Hood

The underlying architecture provides advanced cheminformatics functionalities through a refined interface:

  • Natural Product Analysis: Calculate NP-likeness scores for compounds
  • Similarity Metrics: Compare structures using multiple fingerprinting methods
  • HOSE Code Generation: Generate HOSE codes for structure analysis
  • Chemical Classification: Integrate with ClassyFire for chemical taxonomy
  • Standardisation Workflows: Structure standardisation via ChEMBL pipeline
  • 3D Conformer Generation: Create and visualise 3D molecular structures

Availability & Resources

A public instance of the Cheminformatics Microservice API is hosted at Friedrich Schiller University Jena in Germany, accessible at api.naturalproducts.net. The web application available at app.naturalproducts.net. The source code is available on GitHub and released under the MIT license.

For developers, comprehensive Swagger documentation provides detailed insights into the available APIs. For users new to the platform, the web interface offers an intuitive entry point to explore the full range of capabilities.

Citations

If you use Cheminformatics Microservice in your research or applications, please cite:

Paper:

Software:


Posted on by Theo Bender