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Chemaxon Compound Registration

End-to-end registration out of the box

Compound registration system for the future

Are you ready to stop maintaining a custom-built registration system? Do you need software you can rely on to standardize all input, fix or report errors and keep your compound database in order? 

We have a solution for you. 

Compound Registration provides uniqueness check for different modalities: small molecules including salts, multi-component compounds and polymers, as well as peptides. It comes with a fully functional, preset registration workflow you can customize in detail to fit your business logic. 

You can automatically take compounds through normalization and quality check before registration or intervene in case any criteria are violated. Compound Registration fixes most issues, moving exceptions to a staging area to handle manually. 

Want to get Compound Registration for your team? Book a demo or visit the Chemaxon support portal. 

Structure validation

Compound Registration allows you to apply strict validation and normalization rules on your chemical structures and peptide sequences, then rigorously check for duplications considering stereoisomers, tautomers, isotopes and salt forms. 

Stereochemistry and tautomer handling

Compound Registration’s industry-standard stereochemical and tautomer representation along with its sophisticated multi-component handling ensures that even the most complex compounds are registered with ease. 

Highly performant registration

Compound Registration supports a reliable and performant registration workflow even in the case of multi-million databases and when uploading files with tens of thousands of compounds. 

Bulk registration

Compound Registration provides flexible structure validation and field mapping even when uploading complete compound libraries. It enforces your business rules no matter if your compounds originate from your ELN or are part of a shipment from your CRO. 

Compute supplementary data

Compound Registration automatically populates fields with IUPAC names or selected compound properties during your registration process. No more empty data fields when searching in your compound database. 

Amend registered entities

Compound Registration supports post-registration modifications in case of error correction or misrepresented compounds. Validation and normalization rules are enforced in case of amendments as well, while the compound IDs are properly re-organized according to the structure changes. 

Beyond small molecules

Compound Registration registers peptides based on HELM notation, validating every sequence against your monomer library and automatically generating the corresponding chemical structure. Linear, cyclic and multi-chain peptides are supported, and the capabilities you rely on for small molecules — validation, duplicate checking, bulk upload, amendment and API access — are available for peptides as well. 

Building blocks under control

Compound Registration provides a centrally managed monomer library that serves as the single source of truth for your peptide building blocks. Curate and extend natural and non-natural monomers from the administrative UI, with role-based access control determining who can add or modify monomers, so every HELM-based registration resolves against consistent, approved definitions. 

With Compound Registration, your data is secure

Certara holds ISO 27001 certification for Certara’s Information Security Management System (ISMS). We have implemented robust security controls, undergone rigorous risk assessments, and continuously strive for improvement. Compound Registration ensures full compliance with global data protection standards, offering peace of mind for sensitive analysis.

Learn more in our Trust Center

Why Certara

Certara delivers leading-edge solutions that empower scientists to make data-driven decisions, accelerating drug discovery timelines, and improving outcomes. 

  • Early drug discovery is a core area of expertise at Certara, supported by a team of highly experienced and renowned experts in the field.
  • The dynamic community of users from drug discovery empowers us to continuously refine our solutions to meet the ever-evolving demands of innovative research.

Using Chemaxon’s suite of tools as core components of our chemistry workflows, they save us time while supporting strong, science-driven decisions. What sets them apart is that their team is professional, approachable, and genuinely invested in helping us succeed.

Xin ZhangSr. Director, Cheminformatics and AI/MLCellarity

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Make the most of Compound Registration

Work with our services team dedicated to integrating Compound Registration into your systems. Benefit from expert consultation and training, hands-on guidance with deployment, integration, workflows, data migration and custom development tailored to your business goals.