Resources

Pharos3D Success Stories
Pharos3D Validation
Selected Publications
Video Tutorial and User Manuals
Newsletter Archive
Getting Started with Alipheron Searching Tools
Security Privacy Statement

Pharos3D Success Stories


Pharos3D Validation



Selected Publications


  • T. Sander, J. Freyss, M. von Korff, C. Rufener; DataWarrior: an open-source program for chemistry aware data visualization and analysis, J. Chem. Inf. Model. 55 (2015) 460-473, https://doi.org/10.1021/ci500588j
  • T. Sander, J. Freyss, M. von Korff, J. Rene Reich, C. Rufener; OSIRIS, an Entirely in-House Developed Drug Discovery Informatics System, J. Chem. Inf. Model. 49 (2009) 232-246, https://doi.org/10.1021/ci800305f
  • T. Liphardt, T. Sander, Fast Substructure Search in Combinatorial Library Spaces, J. Chem. Inf. Model. 63 (2023) 5133–5141, https://doi.org/10.1021/acs.jcim.3c00290
  • Ertl P, Patiny L, Sander T, Rufener C, Zasso M; Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia, J. Cheminform. 2015; 7:10, https://doi.org/10.1021/acs.jcim.2c00886
  • J. Hendrickson, T. Sander, COGNOS: A beilstein-type system for organizing organic reactions, J. Chem. Inf. Model. 35 (1995) 251-260, https://doi.org/10.1021/ci00024a015
  • von Korff, Modest, Joel Freyss, and Thomas Sander. “Flexophore, a new versatile 3D pharmacophore descriptor that considers molecular flexibility.”, J. Chem. Inf. Model, 48.4 (2008): 797-810, https://doi.org/10.1021/ci700359j
  • von Korff, Modest, and Thomas Sander. “Molecular complexity calculated by fractal dimension.” Scientific reports 9.1 (2019): 967, https://doi.org/10.1038/s41598-018-37253-8
  • von Korff, Modest, and Thomas Sander. “Toxicity-indicating structural patterns.” J. Chem. Inf. Model 46.2 (2006): 536-544, https://doi.org/10.1021/ci050358k
  • von Korff, Modest, and Thomas Sander. “Limits of prediction for machine learning in drug discovery.” Frontiers in Pharmacology 13 (2022): 832120, http://dx.doi.org/10.3389/fphar.2022.832120
  • Baumann, K., H. Albert, and M. Von Korff. “A systematic evaluation of the benefits and hazards of variable selection in latent variable regression. Part I. Search algorithm, theory and simulations.” Journal of Chemometrics: A Journal of the Chemometrics Society 16.7 (2002): 339-350, https://doi.org/10.1002/cem.730

Video Tutorial and User Manuals


Newsletter Archive


Getting Started with Alipheron Searching Tools


Alipheron plugins facilitates exploration and access to trillions of readily synthesizable molecules in the Alipheron ULCS Collection which is composed of ultra-large combinatorial spaces by well-trusted global suppliers. The process described below used Hyperspace Search as an example, however the getting-started mechanism is the same for all Alipheron plugins.

  1. Download and install DataWarrior. To run trusted plugins, make sure that you obtain DataWarrior version v06.04.01 or newer.
  2. Start DataWarrior and allow automatic update in Help>Update Mode.
  3. Install the Hyperspace plugin: Select Help>Trusted Plugins

  4. Restart DataWarrior; a new menu Alipheron has been created. Select Hyperspace Search....

  5. Register with your name and email to receive a passcode on your given e-mail address.

  6. Enter the pass code in DataWarrior's dialog and that's it! You can start searching! Under the hood you have received a token connected to your e-mail address that is stored locally on your computer and used in the future as access key for Hyperspace searches.

  7. Now select the Library to be searched and select, whether to search for superstructures or structures being similar to your query. Then double-click the Query Structure field to open the structure editor. Here you may draw or paste a (sub)structure or even a chemical name. If you have selected superstructure mode, then you can associate atoms and bonds with query features (select the lasso tool and double click atoms/bonds). You may also attach exclude groups to particular atoms, which are groups that are not allowed at this position.


Security Privacy Statement




1. Data Privacy and Confidentiality

Alipheron maintains a strict policy regarding data privacy: we do not utilize, exploit, or share user data or search results with any third-party entities for any purpose. All user data, queries, search logs, and results remain entirely confidential and are not accessed by Alipheron. The sole exception to this policy occurs in the event of a technical error reported by the user. In such instances, we may request explicit permission to utilize specific search data for debugging purposes.

2. Ownership and Intellectual Property

Alipheron serves exclusively as a provider of software and technical expertise for navigating supplier libraries. Alipheron asserts no claim to ownership, licensing rights, or any other intellectual property interest regarding user-generated data or resulting search data.

3. Technical Security Measures

We employ rigorous security protocols to ensure the integrity of our platform:

  • Encryption: All data processed within Alipheron, as well as all communications between users and our platform, are protected by industry-standard encryption protocols.
  • Access Control: Access to our servers is strictly governed by the principle of least privilege, ensuring that only essential personnel have entry for maintenance purposes.
  • Auditability: Comprehensive documentation regarding our data security measures and independent audits can be provided to partners upon request.

4. Infrastructure and Compliance

Our infrastructure is hosted on secure servers located in Germany and Finland. These services are provisioned by a reputable German-based data center provider, ensuring that all data handling adheres to rigorous European data protection standards (GDPR). Alipheron is formally certified by CyberVadis, a leading French cybersecurity assessment firm. We have achieved a "Mature" rating with a score of 888 out of 1000, reflecting our high standard of cybersecurity readiness.

5. Data Retention and Deletion

Users may initiate a request for the deletion of search data via a written notification to Alipheron.

  • Retention Period: Our standard data retention cycle is three months.
  • Permanent Deletion: Following this duration, all search data is permanently and irrecoverably purged from our systems.
  • Backup Policy: Please be advised that Alipheron does not maintain backup files for search data; once deleted, the data cannot be recovered.