@inproceedings{vandenBroekEppleKuhnetal.2016, author = {van den Broek, Karina and Epple, Matthias and Kuhn, Hubert and Truszkowski, Andreas and Zielesny, Achim}, title = {11th German Conference on Chemoinformatics (GCC 2015). Fulda, Germany. 8-10 November 2015. Mesoscopic simulation of biomolecular systems}, series = {Journal of Cheminformatics}, volume = {8}, booktitle = {Journal of Cheminformatics}, number = {1, Supplement}, issn = {1758-2946}, doi = {10.1186/s13321-016-0119-5}, pages = {O8}, year = {2016}, language = {en} } @inproceedings{BaenschDanielLanigetal.2022, author = {B{\"a}nsch, Felix and Daniel, Mirco and Lanig, Harald and Steinbeck, Christoph and Zielesny, Achim}, title = {A Calculation Pipeline for Differential Molecule Pair Interaction Energies}, series = {35th Molecular Modeling Workshop}, booktitle = {35th Molecular Modeling Workshop}, year = {2022}, language = {en} } @article{RajanBrinkhausSorokinaetal.2021, author = {Rajan, Kohulan and Brinkhaus, Henning Otto and Sorokina, Maria and Zielesny, Achim and Steinbeck, Christoph}, title = {DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature}, series = {Journal of Cheminformatics}, volume = {13}, journal = {Journal of Cheminformatics}, doi = {10.1186/s13321-021-00496-1}, pages = {Artikelnr. 20}, year = {2021}, language = {en} } @misc{Zielesny2019, author = {Zielesny, Achim}, title = {ErtlFunctionalGroupsFinder [Softwarecode, Version 1.0.2.0]}, year = {2019}, abstract = {Ertl algorithm for automated functional groups detection and extraction of organic molecules implemented on the basis of the Chemistry Development Kit (CDK)}, language = {en} } @article{BuschmannWegoZielesnyetal.2006, author = {Buschmann, Hans-J{\"u}rgen and Wego, Andreas and Zielesny, Achim and Schollmeyer, Eckhard}, title = {Structure, Electronic Properties and NMR-Shielding of Cucurbit[n]urils}, series = {Journal of inclusion phenomena and macrocyclic chemistry}, volume = {54}, journal = {Journal of inclusion phenomena and macrocyclic chemistry}, number = {1-2}, issn = {0923-0750}, doi = {10.1007/s10847-005-4602-2}, pages = {85 -- 88}, year = {2006}, language = {en} } @inproceedings{vandenBroekEppleKuhnetal., author = {van den Broek, Karina and Epple, Matthias and Kuhn, Hubert and Zielesny, Achim}, title = {Steps Towards an Open All-in-one Rich-Client Environment for Particle-Based Mesoscopic Simulation}, series = {Konferenz: GCC 2018, 14th German Conference on Chemoinformatics, 11.-13. November 2018 in Mainz}, booktitle = {Konferenz: GCC 2018, 14th German Conference on Chemoinformatics, 11.-13. November 2018 in Mainz}, language = {en} } @inproceedings{StueckenschneiderZielesnySchembecker2012, author = {Stueckenschneider, Kai and Zielesny, Achim and Schembecker, Gerhard}, title = {Adsorption of Alanine and Phenylalanine on MFI-type Zeolite: DFT Calculations and Experimental Results}, series = {Konferenz: 26th Molecular Modelling Workshop 2012. 12.-14. M{\"a}rz 2012 in Erlangen}, booktitle = {Konferenz: 26th Molecular Modelling Workshop 2012. 12.-14. M{\"a}rz 2012 in Erlangen}, year = {2012}, language = {en} } @inproceedings{vandenBroekKuhnZielesnyetal.2016, author = {van den Broek, Karina and Kuhn, Hubert and Zielesny, Achim and Epple, Matthias}, title = {Mesoscopic simulation of the membrane disrupting activity of the cyclotide Kalata B1}, series = {Konferenz: 30th Molecular Modelling Workshop 2016. 4.-6. April 2016 in Erlangen}, booktitle = {Konferenz: 30th Molecular Modelling Workshop 2016. 4.-6. April 2016 in Erlangen}, year = {2016}, language = {en} } @article{RajanBrinkhausAgeaetal.2023, author = {Rajan, Kohulan and Brinkhaus, Henning Otto and Agea, M. Isabel and Zielesny, Achim and Steinbeck, Christoph}, title = {DECIMER.ai: an open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications}, series = {Nature Communications}, volume = {2023}, journal = {Nature Communications}, number = {14: 5045}, doi = {10.1038/s41467-023-40782-0}, year = {2023}, abstract = {The number of publications describing chemical structures has increased steadily over the last decades. However, the majority of published chemical information is currently not available in machine-readable form in public databases. It remains a challenge to automate the process of information extraction in a way that requires less manual intervention - especially the mining of chemical structure depictions. As an open-source platform that leverages recent advancements in deep learning, computer vision, and natural language processing, DECIMER.ai (Deep lEarning for Chemical IMagE Recognition) strives to automatically segment, classify, and translate chemical structure depictions from the printed literature. The segmentation and classification tools are the only openly available packages of their kind, and the optical chemical structure recognition (OCSR) core application yields outstanding performance on all benchmark datasets. The source code, the trained models and the datasets developed in this work have been published under permissive licences. An instance of the DECIMER web application is available at https://decimer.ai.}, language = {en} } @article{vandenBroekDanielEppleetal.2018, author = {van den Broek, Karina and Daniel, Mirco and Epple, Matthias and Schaub, Jonas and Kuhn, Hubert and Zielesny, Achim}, title = {PSMILES - A particle-based Molecular Structure Representation for Mesoscopic Simulation}, series = {Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout, Niederlande}, journal = {Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout, Niederlande}, year = {2018}, language = {en} } @misc{Zielesny2020, author = {Zielesny, Achim}, title = {Computational Intelligence Packages (CIP) for Mathematica [Softwarecode, Version 3.1]}, year = {2020}, language = {en} } @inproceedings{vandenBroekKuhnZielesnyetal.2017, author = {van den Broek, Karina and Kuhn, Hubert and Zielesny, Achim and Epple, Matthias}, title = {Improved Plasma Membrane Models as Test Systems for the Membrane Disrupting Activity of Kalata B1}, series = {Konferenz: 31st Molecular Modelling Workshop 2017. 27.-29. M{\"a}rz 2017 in Erlangen}, booktitle = {Konferenz: 31st Molecular Modelling Workshop 2017. 27.-29. M{\"a}rz 2017 in Erlangen}, year = {2017}, language = {en} } @misc{Zielesny, author = {Zielesny, Achim}, title = {MFsim [Softwarecode, Version 2.5.0.0]}, language = {en} } @misc{Zielesny, author = {Zielesny, Achim}, title = {Jdpd [Softwarecode, Version 1.6.0.0]}, language = {en} } @article{BaenschSchaubSevindiketal.2023, author = {B{\"a}nsch, Felix and Schaub, Jonas and Sevindik, Bet{\"u}l and Behr, Samuel and Zander, Julian and Steinbeck, Christoph and Zielesny, Achim}, title = {MORTAR: a rich client application for in silico molecule fragmentation}, series = {Journal of Cheminformatics}, volume = {2023}, journal = {Journal of Cheminformatics}, number = {15}, publisher = {Springer Nature}, issn = {1758-2946}, doi = {https://doi.org/10.1186/s13321-022-00674-9}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:1010-opus4-42005}, pages = {14}, year = {2023}, abstract = {Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the rules. This requires a computational workflow with data import, fragmentation algorithm integration, and result visualisation. The described workflow is normally unavailable for a new algorithm and must be set up individually. This work presents an open Java rich client Graphical User Interface (GUI) application to support the development of new in silico molecule fragmentation algorithms and make them readily available upon release. The MORTAR (MOlecule fRagmenTAtion fRamework) application visualises fragmentation results of a set of molecules in various ways and provides basic analysis features. Fragmentation algorithms can be integrated and developed within MORTAR by using a specific wrapper class. In addition, fragmentation pipelines with any combination of the available fragmentation methods can be executed. Upon release, three fragmentation algorithms are already integrated: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator. These algorithms, as well as all cheminformatics functionalities in MORTAR, are implemented based on the Chemistry Development Kit (CDK).}, language = {en} } @article{vandenBroekDanielEppleetal.2020, author = {van den Broek, Karina and Daniel, Mirco and Epple, Matthias and Hein, Jan-Mathis and Kuhn, Hubert and Neumann, Stefan and Truszkowski, Andreas and Zielesny, Achim}, title = {MFsim — an open Java all-in-one rich-client simulation environment for mesoscopic simulation}, series = {Journal of Cheminformatics}, volume = {12}, journal = {Journal of Cheminformatics}, issn = {1758-2946}, doi = {10.1186/s13321-020-00432-9}, pages = {29}, year = {2020}, language = {en} } @article{TruszkowskiDanielKuhnetal.2014, author = {Truszkowski, Andreas and Daniel, Mirco and Kuhn, Hubert and Neumann, Stefan and Steinbeck, Christoph and Zielesny, Achim and Epple, Matthias}, title = {A molecular fragment cheminformatics roadmap for mesoscopic simulation}, series = {Journal of Cheminformatics}, volume = {6}, journal = {Journal of Cheminformatics}, number = {Artikelnr. 45}, issn = {1758-2946}, doi = {10.1186/s13321-014-0045-3}, pages = {13}, year = {2014}, language = {en} } @misc{Zielesny2019, author = {Zielesny, Achim}, title = {Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics [Softwarecode, Version 1.1.1.0]}, year = {2019}, abstract = {An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics}, language = {en} } @inproceedings{KuhnNeumannSteinbecketal.2009, author = {Kuhn, Hubert and Neumann, Stefan and Steinbeck, Christoph and Wittekindt, Carsten and Zielesny, Achim}, title = {Molecular fragments chemoinformatics}, series = {Journal of Cheminformatics}, volume = {2}, booktitle = {Journal of Cheminformatics}, number = {Suppl 1}, issn = {1758-2946}, doi = {10.1186/1758-2946-2-S1-P14}, pages = {P14}, year = {2009}, language = {en} } @article{KuhnSteinbeckZielesny2010, author = {Kuhn, Thomas and Steinbeck, Christoph and Zielesny, Achim}, title = {Open-Source-Workflows}, series = {Nachrichten aus der Chemie}, volume = {58}, journal = {Nachrichten aus der Chemie}, number = {1}, issn = {1439-9598}, pages = {40 -- 42}, year = {2010}, language = {de} } @unpublished{ZielesnyWeissenbornLedereretal.2025, author = {Zielesny, Achim and Weißenborn, Viktor and Lederer, Laurin and Steinbeck, Christoph and Rajan, Kohulan}, title = {MARCUS: Molecular Annotation and Recognition for Curating Unravelled Structures}, series = {ChemRxiv}, journal = {ChemRxiv}, doi = {10.26434/chemrxiv-2025-9p1q1}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:1010-opus4-48310}, year = {2025}, abstract = {The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions operate in isolation, which limits their scalability for comprehensive literature curation. Here we present MARCUS (Molecular Annotation and Recognition for Curating Unravelled Structures), a tool to aid curators in performing literature curation in the field of natural products. This integrated web-based platform combines automated text annotation, multi-engine OCSR, and direct submission capabilities to the COCONUT database. MARCUS employs a fine-tuned GPT-4 model to extract chemical entities and utilises an ensemble approach integrating DECIMER, MolNexTR, and MolScribe for structure recognition. The platform aims to streamline the data extraction workflow from PDF upload to database submission, significantly reducing curation time. MARCUS bridges the gap between unstructured chemical literature and machine-actionable databases, enabling FAIR data principles and facilitating AI-driven chemical discovery. Through open-source code, accessible models, and comprehensive documentation, the web application enhances accessibility and promotes community-driven development. This approach facilitates unrestricted use and encourages the collaborative advancement of automated chemical literature curation tools. We dedicate MARCUS to Dr Marcus Ennis, the longest-serving curator of the ChEBI database, on the occasion of his 75th birthday.}, language = {en} }