Patrick Penner

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Whether a molecule is currently patented, or has ever been patented, is a surprisingly difficult question. In my master's thesis I developed a set of tools, for example a knime node, to automatically extract patent information for molecules based on the SureChEMBL dataset.

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Publications: Master's Thesis
Code: Closed Source (inte:ligand)

Cheminformatics InChI SureChEMBL Java PostgreSQL MySQL

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Halogen bonding is a somewhat controversial protein-ligand interaction. Nonetheless, it can be useful in very specific pharmacophore searches. This feature was implemented in inte:ligand's LigandScout Molecular Design Platform.

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Code: Closed Source (inte:ligand)

Java Pharmacophores Halogen Bonding Interactions Structure-based

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FastGrow is a fast shape-based method for structure-based fragment growing. It uses the RVM shape descriptor to generate poses, a pharmacophore-like interaction mode, and the JAMDA scoring function.

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Publications: RVM Shape Descriptors
Code: Closed Source (Group of Matthias Rarey)

Shape-based Structure-based Data-driven Geometric algorithms Pharmacophores C++ PostgreSQL SQLite

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An open source webserver for fragment growing using FastGrow. It is intended as a low barrier to entry way to try out various features of FastGrow.

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Code: Backend Frontend

Javascript Python

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I inherited the Torsion Library project during my doctoral thesis and reworked large parts of it, most visibly the tooling.

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Publications: Torsion Library
Code: Closed Source (Group of Matthias Rarey)

Structure-based Knowledge-based Conformations Structure quality C++ Python

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An open source webserver for evaluating molecule conformations using the Torsion Analyzer. The Torsion Analyzer itself is a commandline tool. This server breaches the gap to the user with a proper visualization of its results.

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Code: Backend Frontend

Python Javascript

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I was involved in sanity checking my colleague Louis Bellmann's chemistry, as well as fruitful discussion about the subgraph enumeration algorithm.

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Publications: CSFP
Code: Closed Source (Group of Matthias Rarey)

C++ Fingerprints Chemical similarity

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SpaceLight is very much Louis Bellmann's achievement. I was mostly there to sanity check chemistry, but also to consider parts of the algorithm itself.

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Publications: SpaceLight
Code: Closed Source (Group of Matthias Rarey)

C++ Combinatorics Fingerprints

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I was one of the first users of JAMDA. My feedback about the results and the code led to several improvements, such as restrained optimization, though clearly most of the credit belongs to Florian Flachsenberg.

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Publications: JAMDA Scoring
Code: Closed Source (Group of Matthias Rarey)

C++ Scoring Ranking Optimization