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Roland W. Knispel
Project Manager

When Is a Large Biomolecule a Small Molecule? - Compound Databases with a Twist


Most organizations maintain multiple registration systems and entity stores for small molecules and biologics, such as: oligonucleotides, proteins, antibodies, antibody-drug conjugates – which increasingly contain unnatural or chemically-modified components. Based on complex business rules, a submission might not end up in the same system it was submitted to, thus making it hard for researchers to track progress of their entities. An attempt to alleviate this is to replicate entity information in multiple systems, but we all know that data duplication is a pattern best avoided.

If a therapeutic peptide is seen as a small molecule structure or an amino acid sequence, depending on the question we ask, it should not rely on the file format we choose to communicate with. We will demonstrate tools which enable perception of biological sequences and its chemical modifications from chemical structure files. Further, full format round-tripping between sequence and chemistry is possible. We have adopted HELM, a notation standard for sequence-derived molecules, across all our tools – as it is able to capture both views within one notation.

In the second step, we will demonstrate how to leverage this technology to deliver truly type-agnostic entity registration systems and entity stores. We will demonstrate scenarios consolidating multiple systems into a single system by using our tools; thereby simplifying processes for researchers, while reducing maintenance costs for IT support groups.

Sign up for our webinar to learn how ChemAxon technology can assist you in closing the gap between small and large molecules in your informatics environment.

Presented by

Roland W. Knispel

Project Manager

Roland W. Knispel obtained his PhD in Structural Biology from the Technical University in Munich for work performed in the group of Wolfgang Baumeister at the Max Planck Institute of Biochemistry in Martinsried. During the time, he gained experience in proteomics studies, activity assays and single particle structural analysis of protein complexes using cryo electron microscopy.

He joined ChemAxon as a Business Analyst in 2012 and one year later became the Technical Project Lead for extending ChemAxon's cheminformatics platform to the world of Biologics.

In 2012, he and his team joined the HELM project of the Pistoia Alliance, and since that time contribute to the development of the HELM standard, enabling standardized and unambiguous representation of a wide range of novel biological modalities encountered in today's R&D activities.

Learning objectives
  • Understand the risks of siloed compound databases
  • Understand, why perception is key to classify molecule types and to ensure data consistency across your databases
  • Learn how HELM helps to standardize the description of biomolecules
  • Learn about concepts to bridge small and large molecule registration systems
  • Vice President Informatics
  • Associate Director Cheminformatics
  • Director IT
  • LRL Research Dedicated
  • Biology IT systems
  • Research Consultant
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  • Director Biologics and Applied Genomics Technologies
  • R&D IS Head of Solution Center Biologics
  • Systems Architect Drug Discovery
  • IT Research
  • Director Research Business Technologies
  • Manager Research Informatics
  • Staff Scientist
  • Scientist I / Scientist II
  • Protein Scientist
  • Protein Chemist
  • Protein Engineering
  • Scientist Synthetic Biology
  • Director Antibody Engineering
  • Director Biologics R&D
  • Scientist Bioconjugates
  • Scientific Group leader
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