Biologics Representation and Search

Therapeutics Are Evolving

The diseases researchers hope to tackle today demand specificity. The growing requirements for outcome-based treatment are shrinking potential patient populations, and researchers must attack increasingly specific targets.

As a result, the industry has expanded the scope of the classes of molecules considered as therapeutic candidates. Peptides, antibodies, antibody-drug conjugates, and more are seizing ever larger shares of life science pipeline. As of 2017, 7 of the top 10 pharmaceutical products by revenue were biologics.

While these classes of therapeutics offer significant opportunities for industry leaders, this has also created an issue for many of the scientifically-aware informatics solutions they rely on. Tools designed to support small molecule structures and data lack the robustness to adequately manage the increasingly complex data biomolecules generate.

BIOVIA Self-Contained Sequence Representation

Between natural and synthetic posttranscriptional modifications, crosslinks, cyclic structures, and synthetic amino acids and nucleotides, organizations need to move beyond text-based sequences and bulky file formats to properly manage their unique biotherapeutic portfolio.

BIOVIA Self-Contained Sequence Representation (SCSR) provides a hybrid representation of biological molecules to support robust entity registration and search. Standard amino acids and nucleotides utilize common templates and labels, while chemical modifications are handled using explicit chemistry. This ensures a compact representation while providing the customization that today’s researchers need.

SCSR streamlines biotherapeutics research by allowing researchers to:

• Share compact, complete chemical representation
• Support interdisciplinary research with a single representation for each entity
• Represent bridges, chains and attachment points
• Create custom residues, linkers, bases, and sugars with BIOVIA Draw
• Search full sequences and substructures using sequence and/or chemical information

Rapidly Register and Search Complex Biomolecules

SCSR builds upon BIOVIA’s extensive history of cheminformatics expertise to provide powerful searching capabilities for biomolecules. Researchers can feel confident that they can find the entities they need, when they need it.

• Substructure searching finds chemically identical regions, regardless of how they are represented (e.g. full chemistry, biopolymer, SCSR, etc.)
• Sequence text search supports querying natural unmodified residues and sequences
• Complements existing sequence searching tools (BLAST, FASTA, etc.)
• Fast-Search indexing of areas with explicit chemistry searching ensures consistent and scalable performance
• Templates capture attachment point information, removing ambiguity in cyclic and crosslinked structures

SCSR Compatibility

Other file formats, such as HELM (developed by the Pistoia Alliance), offer string notation to represent macromolecules. BIOVIA natively supports the automated interconversion between HELM and SCSR. This ensures that the best of both offerings are easily captured and shared throughout your organization.

Support for SCSR with optional HELM interconversion runs throughout the BIOVIA portfolio:

BIOVIA Pipeline Pilot

◾ Macromolecules, SCSR and HELM interconversion components
◾ HTML Sequence Viewer (display SCSR details)
◾ Create and manage with the Centralized Library for custom Residues, linkers etc
◾ Pipette Sketcher and HELM Editor integration
◾ Perceive sequence
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BIOVIA ScienceCloud

◾ HELM to SCSR conversion via the BIOVIA Direct database
◾ Pipette Sketcher and HELM Editor integration
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BIOVIA Registration

◾ Store, depict and search SCSR biologics
◾ Pipette Sketcher and HELM Editor integration
◾ Convert HELM to SCSR structures
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BIOVIA Direct

◾ Store, depict and search SCSR
◾ Synchronize Direct with the Centralized Library
◾ Registration, import and export HELM and XHELM
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BIOVIA Draw

◾ Create SCSR biologics
◾ Synchronize Draw with the Centralized Library
◾ Import and Export HELM Strings and XHELM
◾ HELM Editor integration
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BIOVIA Pipette Sketcher

◾ HELM Editor
◾ SCSR interconversion
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BIOVIA Insight

◾ Search and depict SCSR biologics
◾ Pipette Sketcher and HELM Editor integration
◾ Convert HELM to SCSR structures
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BIOVIA Insight for Excel

◾ Search and depict SCSR biologics
◾ Convert HELM to/from SCSR structures
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ⁱ https://www.statista.com/statistics/258022/top-10-pharmaceutical-products-by-global-sales-2011/