BIOVIA’s Role in Advancing Chemistry Data Representation
For over 30 years, BIOVIA has been a pioneer in advancing chemistry data representation and manipulation. The company invented and continues to update the industry standard file formats: mol, rxn, SDFile, RDFile and XDfile. With tools like BIOVIA Draw, BIOVIA Direct and BIOVIA Pipeline Pilot, they contribute significantly to the scientific community’s arsenal of cutting-edge informatics environments. BIOVIA Chemistry, equipped with features to sketch, store, and retrieve complex molecules takes center stage in providing comprehensive support for diverse research needs.
Chemical Representation
BIOVIA offers two sketchers for sketching molecules, reactions and sequences – BIOVIA Draw and Pipette Sketcher. BIOVIA Draw, a customizable .NET desktop application, is used daily by tens of thousands of scientists. Building on decades of support, it allows researchers to accurately and chemically correctly sketch their scientific entities for registration or queries.
For the past two decades, BIOVIA has provided web-based sketchers. JDraw was very popular and later was replaced with our JS offering, Pipette Sketcher, a modern JavaScript sketcher, which is connected to Pipeline Pilot Chemistry and provides the same chemistry intelligence as BIOVIA Draw.
The Pipette Sketcher has a unique chemistry aware, data-centric user interface that has been proven to be quicker and less error prone for users than traditional sketchers. This has been extended to support peptides and RNA with seamless switching between SCSR and HELM formats.
Additionally, Pipette Sketcher can be configured to support different sketching workflows based on the needs of the web applications that embed it. These workflows include:
- Sketch anything: reactions, small molecules and sequences [for sequences it uses an easy-to-use HELM editor] (Fig 1).
- Exclusively sketch small molecules and reactions.
- Exclusively sketch small molecules with reaction sketching disabled [ideal for molecule registration] (Fig 2).
Please see Pipette Sketcher Blog for more details.
Introducing “Traditional Mode” for Enhanced Sketching Flexibility in Pipette
Today, we’re excited to share an important update. We’re introducing a new feature in Pipette that enables users familiar with other sketchers to draw molecules and reactions in their preferred way.
Users will be able to decide whether they want to sketch in Pipette using the context sensitive chemically aware mode (as they have for the past decade) or switch the user interface to an established, tool-centric sketching experience like BIOVIA Draw and other popular chemical sketchers.
We refer to this new option for sketching as the “traditional mode”, which provides the familiar tool bars for common actions, bonds and atoms, templates and a responsive feedback area.
Drawing and Editing Tools
The Pipette sketcher provides an intuitive drawing interface with various tools for creating and modifying chemical structures, including drawing tools, templates, and shortcuts.
Pipette Sketcher provides the same chemistry and sketching capabilities as BIOVIA Draw including:
- Relative and enhanced stereochemistry for
- Tetrahedral
- Axial
- Higher order stereochemistry
- Geometric
- Repeat units (S-groups and Data S-groups)
- R-groups
- Haptic and Markush bonds
- Abbreviations
- Query features (atom and bond)
- Reactions (automatic layout)
Cross-platform compatibility:
- As Pipette Sketcher is fully web-based, no browser plugins or add-ins are required and is available across different operating systems and devices.
Pipette Sketcher “modern mode” is easy to use on touch devices including:
- iOS and Android
- Windows tablets and touchscreen laptops
Integration with other tools:
- BIOVIA Pipette Sketcher supports applications on the DS 3DEXPERIENCE platform and it can be used with other BIOVIA applications. It is also easily integrated into custom web or custom desktop applications and other external organization’s applications through its tried-and-tested API.
Structure manipulation:
- Pipette supports various structure manipulations, such as converting between different formats (name to structure, HELM, RInChI, SMILES, mol, skc, rxn, cdx, sdf, rdf, xdf), and cleaning up structures.
Sharing and collaboration:
- It allows for easy sharing of chemical structures through various file formats, including image creation, enabling collaboration and knowledge sharing.
Conclusion
BIOVIA Pipette Sketcher now offers both the familiar sketching experience of BIOVIA Draw and other popular chemistry sketching tools, as well as a modern, data-centric, chemistry-aware sketching experience refined through usability studies. Regardless of the experience a user selects, they enjoy the flexibility and accessibility of a web-based application seamlessly integrated with their other tools. This builds upon BIOVIA’s existing tools, providing users with an additional convenient and efficient solution for sketching, sharing, and collaborating on chemical structures and reactions.
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Matthew Sage Dr. Matthew Sage is Senior Product Manager for the Cheminformatics applications at BIOVIA, with over 25 years of experience working with customers in Implementation Project management, Database administration, End User and Administrative training, Custom Software solution deployment and now is responsible for the Cheminformatics portfolio from BIOVIA. Namely the scientific sketchers, chemistry storage and searching capabilities, Pipeline Pilot Chemistry and the Chemistry aspects in BIOVIA’s ELNs. Matthew has a PhD from the University of Bath, UK in Medicinal Chemistry and Molecular Modelling.