TY - INPR A1 - Kullik, Hannah A1 - Urban, Martin A1 - Schaub, Jonas A1 - Loidl-Stahlhofen, Angelika A1 - Zielesny, Achim T1 - PySSA: end-user protein structure prediction and visual analysis with ColabFold and PyMOL N2 - Computational methods for the accurate prediction of protein folding based on amino acid sequences have been researched for decades. The field has been significantly advanced in recent years by deep learning-based approaches, like AlphaFold, RoseTTAFold, or ColabFold. Although these can be used by the scientific community in various, mostly free and open ways, they are not yet widely used by bench scientists in relevant fields such as protein biochemistry or molecular biology, who are often not familiar with software tools such as scripting notebooks, command-line interfaces or cloud computing. In addition, visual inspection functionalities like protein structure displays, structure alignments, and specific protein hotspot analyses are required as a second step to interpret and apply the predicted structures in ongoing research studies. PySSA (Python rich client for visual protein Sequence to Structure Analysis) is an open Graphical User Interface (GUI) application combining the protein sequence to structure prediction capabilities of ColabFold with the open-source variant of the molecular structure visualisation and analysis system PyMOL to make both available to the scientific end-user. PySSA enables the creation of managed and shareable projects with defined protein structure prediction and corresponding alignment workflows that can be conveniently performed by scientists without specialised computer skills or programming knowledge on their local computers. Thus, PySSA can help make protein structure prediction more accessible for end-users in protein chemistry and molecular biology as well as be used for educational purposes. It is openly available on GitHub, alongside a custom graphical installer executable for the Windows operating system: https://github.com/urban233/PySSA/wiki/Installation-for-Windows-Operating-System. To demonstrate the capabilities of PySSA, its usage in a protein mutation study on the protein drug Bone Morphogenetic Protein 2 (BMP2) is described: the structure prediction results indicate that the previously reported BMP2-2Hep-7M mutant, which is intended to be less prone to aggregation, does not exhibit significant spatial rearrangements of amino acid residues interacting with the receptor. KW - protein structure prediction KW - AlphaFold, ColabFold, PyMOL KW - Bone Morphogenetic Protein, BMP, BMP2 Y1 - 2024 U6 - https://doi.org/10.26434/chemrxiv-2024-srx5d ER - TY - JOUR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture JF - Journal of Cheminformatics N2 - Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information in traditional laboratory notebooks or facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. A benchmark was performed using a real-world dataset of hand-drawn chemical structures to evaluate the model's performance. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches. KW - DECIMER KW - Hand-drawn chemical structures KW - OCSR, Optical Chemical Structure Recognition KW - Transformer KW - Deep Learning Y1 - 2024 U6 - https://doi.org/10.1186/s13321-024-00872-7 VL - 2024 IS - 16: 78 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Hein, Jan-Mathis A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Molecule Set Comparator (MSC): a CDK-based open rich‐client tool for molecule set similarity evaluations JF - Journal of Cheminformatics Y1 - 2021 U6 - https://doi.org/10.1186/s13321-021-00485-4 SN - 1758-2946 VL - 13 SP - Artikelnr. 5 ER - TY - CHAP A1 - Truszkowski, Andreas A1 - Fiethen, Annamaria A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Extension of molecular fragment based mesoscopic simulation to the biopolymer realm T2 - Konferenz: 28th Molecular Modelling Workshop 2014. 17.-19. März 2014 in Erlangen Y1 - 2014 ER - TY - CHAP A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Mesoscopic simulation of the membrane disrupting activity of the cyclotide Kalata B1 T2 - Konferenz: GCC 2016, 12th German Conference on Chemoinformatics, 06.-08. November 2016 in Fulda Y1 - 2016 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Weißenborn, Viktor A1 - Lederer, Laurin A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - MARCUS: molecular annotation and recognition for curating unravelled structures JF - Digital Discovery N2 - 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 designed for natural product literature curation that integrates COCONUT-aware schema mapping, CIP-based stereochemical validation, and human-in-the-loop structure refinement. 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 a Human-in-the-loop 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. Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:1010-opus4-49019 VL - 2025 IS - 4 SP - 3137 EP - 3148 PB - Royal Society of Chemistry ER - TY - INPR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Advancements in Hand-Drawn Chemical Structure Recognition through an Enhanced DECIMER Architecture N2 - Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information found in traditional laboratory notebooks or for facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. To evaluate the model's performance, a benchmark was performed using a real-world dataset of hand-drawn chemical structures. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches. KW - OCSR, Optical Chemical Structure Recognition KW - DECIMER KW - Deep Learning KW - Transformer Y1 - 2024 U6 - https://doi.org/10.26434/chemrxiv-2024-7ch9f ER - TY - INPR A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - STOUT V2.0: SMILES to IUPAC name conversion using transformer models T2 - ChemRxiv N2 - Naming chemical compounds systematically is a complex task governed by a set of rules established by the International Union of Pure and Applied Chemistry (IUPAC). These rules are universal and widely accepted by chemists worldwide, but their complexity makes it challenging for individuals to consistently apply them accurately. A translation method can be employed to address this challenge. Accurate translation of chemical compounds from SMILES notation into their corresponding IUPAC names is crucial, as it can significantly streamline the laborious process of naming chemical structures. Here, we present STOUT (SMILES-TO-IUPAC-name translator) V2.0, which addresses this challenge by introducing a transformer-based model that translates string representations of chemical structures into IUPAC names. Trained on a dataset of nearly 1 billion SMILES strings and their corresponding IUPAC names, STOUT V2.0 demonstrates exceptional accuracy in generating IUPAC names, even for complex chemical structures. The model's ability to capture intricate patterns and relationships within chemical structures enables it to generate precise and standardised IUPAC names. Deterministic algorithms for systematically naming chemical structures have been available for many years. Also, this work has only been possible through an academic license for OpenEye’s Lexichem software. KW - Transformers KW - Deep Learning KW - Artificial Intelligence KW - Chemical name translation Y1 - 2024 U6 - https://doi.org/10.26434/chemrxiv-2024-089vs ER - TY - JOUR A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package JF - Journal of Cheminformatics N2 - An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. KW - Intermolecular interaction KW - Nonbonding interaction KW - Molecular Force Field KW - Molecular modeling KW - Molecular Dynamics Y1 - 2024 U6 - https://doi.org/10.1186/s13321-024-00890-5 VL - 16 (2024) IS - Artikel Nr. 96 ER - TY - CHAP A1 - Zielesny, Achim A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph T1 - An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package T2 - 36th Molecular Modeling Workshop, Erlangen, Germany N2 - An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLSAA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Y1 - 2024 N1 - Poster Session, Abstract und Poster im Tagungsband veröffentlicht. ER - TY - CHAP A1 - van den Broek, Karina A1 - Epple, Matthias A1 - Kuhn, Hubert A1 - Truszkowski, Andreas A1 - Zielesny, Achim T1 - 11th German Conference on Chemoinformatics (GCC 2015). Fulda, Germany. 8–10 November 2015. Mesoscopic simulation of biomolecular systems T2 - Journal of Cheminformatics Y1 - 2016 U6 - https://doi.org/10.1186/s13321-016-0119-5 SN - 1758-2946 VL - 8 IS - 1, Supplement SP - O8 ER - TY - CHAP A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - A Calculation Pipeline for Differential Molecule Pair Interaction Energies T2 - 35th Molecular Modeling Workshop Y1 - 2023 N1 - Poster Session, Abstract im Tagungsband veröffentlicht. ER - TY - JOUR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Sorokina, Maria A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature JF - Journal of Cheminformatics Y1 - 2021 U6 - https://doi.org/10.1186/s13321-021-00496-1 VL - 13 SP - Artikelnr. 20 ER - TY - GEN A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder [Softwarecode, Version 1.0.2.0] N2 - Ertl algorithm for automated functional groups detection and extraction of organic molecules implemented on the basis of the Chemistry Development Kit (CDK) Y1 - 2019 UR - https://github.com/zielesny/ErtlFunctionalGroupsFinder/releases/tag/V1.0.2.0 ER - TY - JOUR A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Structure, Electronic Properties and NMR-Shielding of Cucurbit[n]urils JF - Journal of inclusion phenomena and macrocyclic chemistry Y1 - 2006 U6 - https://doi.org/10.1007/s10847-005-4602-2 SN - 0923-0750 VL - 54 IS - 1-2 SP - 85 EP - 88 ER - TY - CHAP A1 - van den Broek, Karina A1 - Epple, Matthias A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - Steps Towards an Open All-in-one Rich-Client Environment for Particle-Based Mesoscopic Simulation T2 - Konferenz: GCC 2018, 14th German Conference on Chemoinformatics, 11.-13. November 2018 in Mainz Y1 - 2018 ER - TY - CHAP A1 - Stueckenschneider, Kai A1 - Zielesny, Achim A1 - Schembecker, Gerhard T1 - Adsorption of Alanine and Phenylalanine on MFI-type Zeolite: DFT Calculations and Experimental Results T2 - Konferenz: 26th Molecular Modelling Workshop 2012. 12.-14. März 2012 in Erlangen Y1 - 2012 ER - TY - CHAP A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Mesoscopic simulation of the membrane disrupting activity of the cyclotide Kalata B1 T2 - Konferenz: 30th Molecular Modelling Workshop 2016. 4.-6. April 2016 in Erlangen Y1 - 2016 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Agea, M. Isabel A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - DECIMER.ai: an open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications JF - Nature Communications N2 - 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. KW - machine learning KW - artificial intelligence KW - AI KW - optical chemical structure recognition KW - OCSR Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40782-0 VL - 2023 IS - 14: 5045 ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Schaub, Jonas A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - PSMILES – A particle-based Molecular Structure Representation for Mesoscopic Simulation JF - Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout, Niederlande Y1 - 2018 UR - http://www.int-conf-chem-structures.org/fileadmin/user_upload/ICCS_2018/posters/P76-Zielesny.pdf ER - TY - GEN A1 - Zielesny, Achim T1 - Computational Intelligence Packages (CIP) for Mathematica [Softwarecode, Version 3.1] Y1 - 2020 UR - https://github.com/zielesny/CIP/releases/tag/3.0 ER - TY - CHAP A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Improved Plasma Membrane Models as Test Systems for the Membrane Disrupting Activity of Kalata B1 T2 - Konferenz: 31st Molecular Modelling Workshop 2017. 27.-29. März 2017 in Erlangen Y1 - 2017 ER - TY - GEN A1 - Zielesny, Achim T1 - MFsim [Softwarecode, Version 2.5.0.0] Y1 - 2022 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd [Softwarecode, Version 1.6.0.0] Y1 - 2022 ER - TY - JOUR A1 - Bänsch, Felix A1 - Schaub, Jonas A1 - Sevindik, Betül A1 - Behr, Samuel A1 - Zander, Julian A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - MORTAR: a rich client application for in silico molecule fragmentation JF - Journal of Cheminformatics N2 - 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). KW - Chemistry Development Kit KW - CDK KW - Molecule fragmentation KW - In silico fragmentation KW - Scaffolds KW - Functional groups KW - Glycosidic moieties KW - Rich client KW - Graphical user interface KW - GUI Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:1010-opus4-42005 SN - 1758-2946 VL - 2023 IS - 15 PB - Springer Nature ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Hein, Jan-Mathis A1 - Kuhn, Hubert A1 - Neumann, Stefan A1 - Truszkowski, Andreas A1 - Zielesny, Achim T1 - MFsim — an open Java all-in-one rich-client simulation environment for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2020 U6 - https://doi.org/10.1186/s13321-020-00432-9 SN - 1758-2946 VL - 12 SP - 29 ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Daniel, Mirco A1 - Kuhn, Hubert A1 - Neumann, Stefan A1 - Steinbeck, Christoph A1 - Zielesny, Achim A1 - Epple, Matthias T1 - A molecular fragment cheminformatics roadmap for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2014 U6 - https://doi.org/10.1186/s13321-014-0045-3 SN - 1758-2946 VL - 6 IS - Artikelnr. 45 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics [Softwarecode, Version 1.1.1.0] N2 - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics Y1 - 2019 UR - https://github.com/zielesny/Jdpd/releases/tag/1.1.1.0 ER - TY - CHAP A1 - Kuhn, Hubert A1 - Neumann, Stefan A1 - Steinbeck, Christoph A1 - Wittekindt, Carsten A1 - Zielesny, Achim T1 - Molecular fragments chemoinformatics T2 - Journal of Cheminformatics Y1 - 2009 U6 - https://doi.org/10.1186/1758-2946-2-S1-P14 SN - 1758-2946 VL - 2 IS - Suppl 1 SP - P14 ER - TY - JOUR A1 - Kuhn, Thomas A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Open-Source-Workflows JF - Nachrichten aus der Chemie Y1 - 2010 SN - 1439-9598 VL - 58 IS - 1 SP - 40 EP - 42 ER - TY - INPR A1 - Zielesny, Achim A1 - Weißenborn, Viktor A1 - Lederer, Laurin A1 - Steinbeck, Christoph A1 - Rajan, Kohulan T1 - MARCUS: Molecular Annotation and Recognition for Curating Unravelled Structures T2 - ChemRxiv N2 - 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. Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:hbz:1010-opus4-48310 ER - TY - INPR A1 - Brinkhaus, Henning Otto A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - RanDepict - Random Chemical Structure Depiction Generator T2 - ChemRxiv N2 - The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others. Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions. Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options. By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems. Y1 - 2022 U6 - https://doi.org/10.26434/chemrxiv-2022-t1kbb ER - TY - JOUR A1 - van den Broek, Karina A1 - Epple, Matthias A1 - Kersten, Lisa Sophie A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation JF - Journal of Chemical Information and Modeling Y1 - 2021 U6 - https://doi.org/10.1021/acs.jcim.1c00332 SN - 1549-9596 VL - 61 IS - 6 SP - 3027 EP - 3040 ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Fiethen, Annamaria A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD) JF - Journal of Cheminformatics Y1 - 2012 U6 - https://doi.org/10.1186/1758-2946-5-S1-P4 SN - 1758-2946 VL - 5 IS - Suppl 1 SP - P4 ER - TY - JOUR A1 - Kuhn, Thomas A1 - Willighagen, Egon L. A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - CDK-Taverna: an open workflow environment for cheminformatics JF - BMC Bioinformatics Y1 - 2010 U6 - https://doi.org/10.1186/1471-2105-11-159 VL - 11 SP - 159 ER - TY - JOUR A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph A1 - Rajan, Kohulan T1 - DECIMER—hand-drawn molecule images dataset JF - Journal of Cheminformatics N2 - The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER — Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field. Y1 - 2022 SN - 1758-2946 VL - 14.2022 SP - 1 EP - 5 PB - BioMed Central CY - London ER - TY - INPR A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph A1 - Rajan, Kohulan T1 - DECIMER - Hand-drawn molecule images dataset N2 - The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER - Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field. KW - OCSR KW - Hand-drawn images KW - Molecule images KW - Deep learning KW - Chemical structure depictions KW - Optical Chemical Structure Recognition Y1 - 2022 ER - TY - GEN A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder [Softwarecode, Version 1.0.0.0] N2 - The algorithm for automated functional groups detection and extraction of organic molecules developed by Peter Ertl is implemented on the basis of the Chemistry Development Kit (CDK). Folder Basic contains the basic ErtlFunctionalGroupsFinder code and test code for integration in Java projects. Folder CDK contains CDK library jar file cdk-2.2.jar that ErtlFunctionalGroupsFinder works with. Folder Evaluation contains sample code for evaluation of functional groups with ErtlFunctionalGroupsFinder. Folder JUnit 4 contains library jar files for unit testing. Folder Performance contains a jar library for performance tests. ErtlFunctionalGroupsFinder is described in the scientific literature Y1 - 2019 UR - https://github.com/zielesny/ErtlFunctionalGroupsFinder ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Fiethen, Annamaria A1 - Kuhn, Hubert A1 - Wiebringhaus, Thomas A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants JF - Journal of Cheminformatics Y1 - 2014 U6 - https://doi.org/10.1186/1758-2946-6-S1-P9 SN - 1758-2946 VL - 6 IS - Suppl 1 SP - P9 ER - TY - CHAP A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Mesoscopic Simulations: New Membrane Models & Studying the Mechanism of the Cyclotide Kalata B1 and it’s Mutants T2 - Konferenz: GCC 2017, 13th German Conference on Chemoinformatics, 05.-07. November 2017 in Mainz Y1 - 2017 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - STOUT: SMILES to IUPAC names using neural machine translation JF - Journal of Cheminformatics Y1 - 2021 U6 - https://doi.org/10.1186/s13321-021-00512-4 SN - 1758-2946 VL - 13 SP - Artikelnr. 34 ER - TY - JOUR A1 - Kuhn, Thomas A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Open-Source-Workflows JF - Nachrichten aus der Chemie Y1 - 2010 U6 - https://doi.org/10.1002/nadc.201070229 SN - 1439-9598 VL - 58 IS - 1 SP - 40 EP - 42 ER - TY - GEN A1 - Zielesny, Achim T1 - A C# high-performance mathematical function compiler for efficient and fast calculation of function values of arbitrary complex single-line mathematical formulas at design and runtime [Softwarecode, Version 1.0.0.0] N2 - A C# high-performance mathematical function compiler for efficient and fast calculation of function values of arbitrary complex single-line mathematical formulas at design and runtime Y1 - 2018 UR - https://github.com/zielesny/MathCompiler ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Fiethen, Annamaria A1 - Kuhn, Hubert A1 - Wiebringhaus, Thomas A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants JF - Journal of Cheminformatics Y1 - 2014 U6 - https://doi.org/10.1186/1758-2946-6-S1-P9 SN - 1758-2946 VL - 6 IS - Suppl 1 SP - P9 ER - TY - CHAP A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Schaub, Jonas A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - PSMILES – A particle-based Molecular Structure Representation for Mesoscopic Simulation T2 - Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout (Niederlande) Y1 - 2018 ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Kuhn, Hubert A1 - Schaub, Jonas A1 - Zielesny, Achim T1 - SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2018 U6 - https://doi.org/10.1186/s13321-018-0294-7 SN - 1758-2946 IS - 10 SP - 35 ER - TY - CHAP A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - The DECIMER (Deep lEarning for Chemical IMagE Recognition) project BT - May 8 -12, 2022 in Garmisch-Partenkirchen/Germany T2 - 17th German Conference on Cheminformatics Y1 - 2022 PB - Gesellschaft Deutscher Chemiker CY - Frankfurt a.M. ER - TY - CHAP A1 - Truszkowski, Andreas A1 - Fiethen, Annamaria A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Molecular simulations of peptides and proteins with Molecular Fragment Dynamics T2 - Konferenz: 10th International Conference on Chemical Structures & 10th German Conference on Chemoinformatics. 1.-5. Juni 2014 in Noordwijkerhout, Niederlande Y1 - 2014 ER - TY - CHAP A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - The DECIMER (Deep lEarning for Chemical IMagE Recognition) project BT - 12-16 June 2022, Noordwijkerhout, The Netherlands T2 - 12th International Conference on Chemical Structures Y1 - 2022 ER - TY - GEN A1 - Zielesny, Achim T1 - MFsim [Softwarecode, Version 2.4.0.0] Y1 - 2021 ER - TY - GEN A1 - Zielesny, Achim T1 - Computational Intelligence Packages (CIP) for Mathematica [Softwarecode, Version 2.0] N2 - CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities. Y1 - 2018 UR - https://github.com/zielesny/CIP ER - TY - JOUR A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Structure, Stability, Electronic Properties and NMR-Shielding of the Cucurbit[6]uril–Spermine-Complex JF - Journal of inclusion phenomena and macrocyclic chemistry Y1 - 2006 U6 - https://doi.org/10.1007/s10847-005-8140-8 SN - 0923-0750 VL - 54 SP - 241 EP - 246 ER - TY - GEN A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder [Softwarecode, Version 1.0.1.0] N2 - Ertl algorithm for automated functional groups detection and extraction of organic molecules implemented on the basis of the Chemistry Development Kit (CDK) Y1 - 2019 UR - https://github.com/zielesny/ErtlFunctionalGroupsFinder/releases/tag/V1.0.1.0 ER - TY - JOUR A1 - Buschmann, Hans-Jürgen A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Hemicucurbit[6]uril a Macrocyclic Ligand with Unusual Complexing Properties JF - Journal of inclusion phenomena and macrocyclic chemistry Y1 - 2006 U6 - https://doi.org/10.1007/s10847-005-6993-5 SN - 0923-0750 VL - 54 IS - 3-4 SP - 181 EP - 185 ER - TY - CHAP A1 - Stueckenschneider, Kai A1 - Zielesny, Achim A1 - Merz, J. A1 - Schembecker, Gerhard T1 - Adsorption of amino acids in MFI-type zeolite: a computational and experimental study T2 - Konferenz: 15th European Congress on Biotechnology. 23.-26. September 2012 in Istanbul, Türkei Y1 - 2012 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - DECIMER: towards deep learning for chemical image recognition JF - Journal of Cheminformatics Y1 - 2020 U6 - https://doi.org/10.1186/s13321-020-00469-w IS - 12 SP - 65 ER - TY - JOUR A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics JF - Journal of Cheminformatics Y1 - 2018 U6 - https://doi.org/10.1186/s13321-018-0278-7 IS - 10 SP - 25 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd [Softwarecode, Version 1.5.0.0] Y1 - 2021 ER - TY - JOUR A1 - Brinkhaus, Henning Otto A1 - Rajan, Kohulan A1 - Schaub, Jonas A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Open data and algorithms for open science in AI-driven molecular informatics JF - Current Opinion in Structural Biology N2 - Recent years have seen a sharp increase in the development of deep learning and artificial intelligence-based molecular informatics. There has been a growing interest in applying deep learning to several subfields, including the digital transformation of synthetic chemistry, extraction of chemical information from the scientific literature, and AI in natural product-based drug discovery. The application of AI to molecular informatics is still constrained by the fact that most of the data used for training and testing deep learning models are not available as FAIR and open data. As open science practices continue to grow in popularity, initiatives which support FAIR and open data as well as open-source software have emerged. It is becoming increasingly important for researchers in the field of molecular informatics to embrace open science and to submit data and software in open repositories. With the advent of open-source deep learning frameworks and cloud computing platforms, academic researchers are now able to deploy and test their own deep learning models with ease. With the development of new and faster hardware for deep learning and the increasing number of initiatives towards digital research data management infrastructures, as well as a culture promoting open data, open source, and open science, AI-driven molecular informatics will continue to grow. This review examines the current state of open data and open algorithms in molecular informatics, as well as ways in which they could be improved in future. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1016/j.sbi.2023.102542 VL - 2023 IS - 79 ER - TY - JOUR A1 - Schaub, Jonas A1 - Zander, Julian A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK) JF - Journal of Cheminformatics N2 - The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day. KW - Cheminformatics KW - Chemistry Development Kit KW - CDK KW - Natural products KW - Scaffold KW - Scaffold tree KW - Scaffold network KW - Fragmentation KW - Chemical space KW - Clustering Y1 - 2022 U6 - https://doi.org/https://doi.org/10.1186/s13321-022-00656-x SN - 1758-2946 VL - 2022 IS - 14:79 PB - BioMed Central CY - London ER - TY - JOUR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Sorokina, Maria A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature JF - Journal of Cheminformatics Y1 - 2021 U6 - https://doi.org/10.1186/s13321-021-00496-1 SN - 1758-2946 VL - 13 SP - Artikelnr. 20 ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Neumann, Stefan A1 - Zielesny, Achim A1 - Willighagen, Egon L. A1 - Steinbeck, Christoph T1 - CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution JF - Journal of Cheminformatics Y1 - 2011 U6 - https://doi.org/10.1186/1758-2946-3-S1-P5 SN - 1758-2946 VL - 3 IS - Suppl 1 SP - P5 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics [Softwarecode, Version 1.2.0.0] N2 - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics Y1 - 2019 UR - https://github.com/zielesny/Jdpd/releases/tag/1.2.0.0 ER - TY - CHAP A1 - Bänsch, Felix A1 - Schaub, Jonas A1 - Sevindik, Betül A1 - Behr, Samuel A1 - Zander, Julian A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - MORTAR – A Rich Client Application for in silico Molecule Fragmentation T2 - 35th Molecular Modeling Workshop Y1 - 2023 N1 - Poster Session, Abstract im Tagungsband veröffentlicht. ER - TY - JOUR A1 - Buschmann, Hans-Jürgen A1 - Zielesny, Achim T1 - Geometric, electronic and NMR properties of hemicucurbit[n]urils and their anionic complexes JF - Computational and Theoretical Chemistry Y1 - 2013 U6 - https://doi.org/10.1016/j.comptc.2013.08.012 SN - 2210-271X VL - 1022 SP - 14 EP - 22 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Performance of chemical structure string representations for chemical image recognition using transformers JF - Digital Discovery N2 - The use of molecular string representations for deep learning in chemistry has been steadily increasing in recent years. The complexity of existing string representations, and the difficulty in creating meaningful tokens from them, lead to the development of new string representations for chemical structures. In this study, the translation of chemical structure depictions in the form of bitmap images to corresponding molecular string representations was examined. An analysis of the recently developed DeepSMILES and SELFIES representations in comparison with the most commonly used SMILES representation is presented where the ability to translate image features into string representations with transformer models was specifically tested. The SMILES representation exhibits the best overall performance whereas SELFIES guarantee valid chemical structures. DeepSMILES perform in between SMILES and SELFIES, InChIs are not appropriate for the learning task. All investigations were performed using publicly available datasets and the code used to train and evaluate the models has been made available to the public. Y1 - 2022 SN - 2635-098X VL - 1.2022 IS - 1 SP - 84 EP - 90 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Bänsch, Felix A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics JF - Membranes N2 - Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.3390/membranes12060619 VL - 12.2022 IS - 6 SP - 619 PB - MDPI CY - Basel ER - TY - CHAP A1 - van den Broek, Karina A1 - Fiethen, Annamaria A1 - Truszkowski, Andreas A1 - Zielesny, Achim A1 - Kuhn, Hubert T1 - Molecular Fragment Dynamics Study of the Interaction between Zinc Ricinoleate and the Complexing Agent Methylglycinediacetic Acid as a new System for Enzyme Purification T2 - Konferenz: 10th International Conference on Chemical Structures & 10th German Conference on Chemoinformatics. 1.-5. Juni 2014 in Noordwijkerhout, Niederlande Y1 - 2014 ER - TY - JOUR A1 - Fritsch, Sebastian A1 - Neumann, Stefan A1 - Schaub, Jonas A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK) JF - Journal of Cheminformatics Y1 - 2019 U6 - https://doi.org/10.1186/s13321-019-0361-8 VL - 11 SP - 37 ER - TY - JOUR A1 - Truszkowski, Andreas A1 - van den Broek, Karina A1 - Kuhn, Hubert A1 - Zielesny, Achim A1 - Epple, Matthias T1 - Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics JF - Journal of Chemical Information and Modeling Y1 - 2015 U6 - https://doi.org/10.1021/ci5006096 SN - 1549-960X VL - 55 IS - 5 SP - 983 EP - 997 ER - TY - CHAP A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Understanding Cucurbit[6]uril-Spermine T2 - Konferenz: 393. WE-Heraeus-Seminar: Trends in Molecular Biophysical Spectroscopy - Electronic Structure, Function, and Dynamics of Biomolecules. 26.-28. April 2007 in Bad Honnef Y1 - 2007 ER - TY - CHAP A1 - Bänsch, Felix A1 - Schaub, Jonas A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - MORTAR - An open rich-client framework for in silico molecule fragmentation BT - May 8 -12, 2022 in Garmisch-Partenkirchen/Germany T2 - 17th German Conference on Cheminformatics Y1 - 2022 PB - Gesellschaft Deutscher Chemiker e.V. CY - Frankfurt/Main ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd [Softwarecode, Version 1.6.2.0] N2 - From https://github.com/zielesny/Jdpd: Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim. Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version. Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests. Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below). See text file JdpdVersionHistory.txt for a version history with more detailed information. KW - Dissipative Particle Dynamics Y1 - 2024 N1 - Jdpd is open source and available at https://github.com/zielesny/Jdpd ER - TY - JOUR A1 - Bänsch, Felix A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation JF - Journal of Cheminformatics N2 - The influence of molecular fragmentation and parameter settings on a mesoscopic dissipative particle dynamics (DPD) simulation of lamellar bilayer formation for a C10E4/water mixture is studied. A “bottom-up” decomposition of C10E4 into the smallest fragment molecules (particles) that satisfy chemical intuition leads to convincing simulation results which agree with experimental findings for bilayer formation and thickness. For integration of the equations of motion Shardlow’s S1 scheme proves to be a favorable choice with best overall performance. Increasing the integration time steps above the common setting of 0.04 DPD units leads to increasingly unphysical temperature drifts, but also to increasingly rapid formation of bilayer superstructures without significantly distorted particle distributions up to an integration time step of 0.12. A scaling of the mutual particle–particle repulsions that guide the dynamics has negligible influence within a considerable range of values but exhibits apparent lower thresholds beyond which a simulation fails. Repulsion parameter scaling and molecular particle decomposition show a mutual dependence. For mapping of concentrations to molecule numbers in the simulation box particle volume scaling should be taken into account. A repulsion parameter morphing investigation suggests to not overstretch repulsion parameter accuracy considerations. KW - Dissipative particle dynamics, DPD, Surfactant, Bilayer, Lamellar, Simulation, Mesoscopic Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1186/s13321-023-00697-w VL - 2023 IS - 15, 23 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - STOUT V2.0: SMILES to IUPAC name conversion using transformer models JF - Journal of Cheminformatics N2 - Naming chemical compounds systematically is a complex task governed by a set of rules established by the International Union of Pure and Applied Chemistry (IUPAC). These rules are universal and widely accepted by chemists worldwide, but their complexity makes it challenging for individuals to consistently apply them accurately. A translation method can be employed to address this challenge. Accurate translation of chemical compounds from SMILES notation into their corresponding IUPAC names is crucial, as it can significantly streamline the laborious process of naming chemical structures. Here, we present STOUT (SMILES-TO-IUPAC-name translator) V2, which addresses this challenge by introducing a transformer-based model that translates string representations of chemical structures into IUPAC names. Trained on a dataset of nearly 1 billion SMILES strings and their corresponding IUPAC names, STOUT V2 demonstrates exceptional accuracy in generating IUPAC names, even for complex chemical structures. The model’s ability to capture intricate patterns and relationships within chemical structures enables it to generate precise and standardised IUPAC names. While established deterministic algorithms remain the gold standard for systematic chemical naming, our work, enabled by access to OpenEye’s Lexichem software through an academic license, demonstrates the potential of neural approaches to complement existing tools in chemical nomenclature. KW - Artificial Intelligence KW - Machine Learning KW - Transformer KW - SMILES KW - IUPAC names Y1 - 2024 U6 - https://doi.org/10.1186/s13321-024-00941-x VL - 2024 IS - 16:146 ER - TY - JOUR A1 - Rajan, Kohulan A1 - Brinkhaus, Henning Otto A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - A review of optical chemical structure recognition tools JF - Journal of Cheminformatics Y1 - 2020 U6 - https://doi.org/10.1186/s13321-020-00465-0 IS - 12 SP - 603 ER - TY - INPR A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - DECIMER 1.0: Deep Learning for Chemical Image Recognition using Transformers Y1 - 2021 U6 - https://doi.org/10.33774/chemrxiv-2021-9j7wg-v2 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics [Softwarecode, Version 1.0.0.0] Y1 - 2018 UR - https://github.com/zielesny/Jdpd/releases/tag/1.0.0.0 ER - TY - RPRT A1 - Zielesny, Achim A1 - Truszkowski, Andreas A1 - van den Broek, Karina T1 - Ein virtuelles Mikroskop in die biomolekulare Nanowelt T2 - Forschung und Entwicklung an der Westfälischen Hochschule. Forschungsbericht 2014 Y1 - 2014 SP - 45 EP - 46 PB - Westfälische Hochschule CY - Gelsenkirchen ER - TY - INPR A1 - van den Broek, Karina A1 - Epple, Matthias A1 - Kersten, Lisa Sophie A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation Y1 - 2021 U6 - https://doi.org/10.26434/chemrxiv.14135783.v1 ER - TY - JOUR A1 - Schaub, Jonas A1 - Zielesny, Achim A1 - Steinbeck, Christoph A1 - Sorokina, Maria T1 - Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database JF - Biomolecules Y1 - 2021 U6 - https://doi.org/10.3390/biom11040486 SN - 2218-273X VL - 11 IS - 4 SP - 486 ER - TY - BOOK A1 - Zielesny, Achim T1 - From Curve Fitting to Machine Learning. An Illustrative Guide to Scientific Data Analysis and Computational Intelligence Y1 - 2016 SN - 978-3-319-32544-6 U6 - https://doi.org/10.1007/978-3-319-32545-3 PB - Springer International Publishing CY - Cham ET - 2 ER - TY - GEN A1 - Zielesny, Achim T1 - Computational Intelligence Packages (CIP) for Mathematica [Softwarecode, Version 1.0] Y1 - 2011 UR - https://github.com/zielesny/CIP ER - TY - JOUR A1 - Schaub, Christoph A1 - Zielesny, Achim T1 - Plattform für wissenschaftliche Information JF - Nachrichten aus der Chemie Y1 - 2005 U6 - https://doi.org/10.1002/nadc.20050530716 SN - 1439-9598 VL - 53 IS - 7/8 SP - 786 EP - 790 ER - TY - JOUR A1 - Zielesny, Achim A1 - Loidl-Stahlhofen, Angelika A1 - Kullik, Hannah A1 - Urban, Martin A1 - Schaub, Jonas T1 - PySSA for Windows: End-User Protein Structure Prediction and Visual Analysis with ColabFold and PyMOL JF - Journal of Chemical Information and Modeling N2 - PySSA (Python rich client for visual protein Sequence to Structure Analysis) for Windows is a comfortable open Graphical User Interface (GUI) application combining the protein sequence to structure prediction capabilities of ColabFold with the open-source variant of the molecular structure visualization and analysis system PyMOL to make both available to the scientific end-user. PySSA enables the creation and sharing of workflow projects that comprise defined protein 3D structure predictions from their amino acid sequence, protein 3D structure alignments, as well as their visual analysis with distance diagrams or hotspot inspection. All operations can be conveniently performed by scientists without specialized computer skills or even programming knowledge on their local Windows computers, without the need for powerful GPU hardware. Thus, PySSA can help make protein structure prediction more accessible for end-users in scientific research areas like protein chemistry or molecular biology. In addition, the application is well-suited for educational purposes due to its user-friendliness and low learning curve. PySSA is openly available on GitHub, alongside a convenient installer executable for the Windows operating system: https://urban233.github.io/PySSA/install.html. To demonstrate its capabilities, the usage of PySSA in a protein mutation study on the protein drug Bone Morphogenetic Protein 2 (BMP2) is described: the structure prediction results indicate that the previously reported BMP2-2Hep-7M mutant, which is intended to be less prone to aggregation, does not exhibit significant spatial rearrangements of amino acid residues interacting with the receptor. Y1 - 2025 U6 - https://doi.org/10.1021/acs.jcim.5c00797 VL - 2025 IS - 65 SP - 5839 EP - 5846 PB - ACS Publications ER - TY - JOUR A1 - Brinkhaus, Henning Otto A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - RanDepict: Random chemical structure depiction generator JF - Journal of Cheminformatics N2 - The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others. Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions. Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options. By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems. KW - CDK KW - Chemical image depiction KW - Depiction generator image augmentation KW - Indigo KW - RDKit KW - OCSR Y1 - 2022 SN - 1758-2946 VL - 14.2022 IS - 31 SP - 1 EP - 7 PB - BioMed Central CY - London ER - TY - INPR A1 - Schaub, Jonas A1 - Zander, Julian A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Scaffold Generator - A Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK) N2 - The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day. Y1 - 2022 ER - TY - GEN A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder [Softwarecode, Version 1.0.3.0] N2 - Ertl algorithm for automated functional groups detection and extraction of organic molecules implemented on the basis of the Chemistry Development Kit (CDK) Y1 - 2019 UR - https://github.com/zielesny/ErtlFunctionalGroupsFinder/releases/tag/V1.0.3.0 ER - TY - CHAP A1 - Schaub, Jonas A1 - Fritsch, Sebastian A1 - Neumann, Stefan A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK) T2 - Konferenz: 15th German Conference on Cheminformatics GCC 2019, 3.-5. November 2019 in Mainz Y1 - 2019 ER - TY - JOUR A1 - Kuhn, Thomas A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project JF - Chemistry Central Journal Y1 - 2008 U6 - https://doi.org/10.1186/1752-153X-2-S1-P27 SN - 1752-153X VL - 2 IS - Suppl 1 SP - P27 ER - TY - JOUR A1 - Schaub, Jonas A1 - Zielesny, Achim A1 - Steinbeck, Christoph A1 - Sorokina, Maria T1 - Too sweet: cheminformatics for deglycosylation in natural products JF - Journal of Cheminformatics Y1 - 2020 U6 - https://doi.org/10.1186/s13321-020-00467-y IS - 12 SP - 67 ER - TY - GEN A1 - Zielesny, Achim T1 - MFsim [Softwarecode, Version 2.3.0.0] Y1 - 2021 UR - https://github.com/zielesny/MFsim/releases/tag/2.3.0.0 ER - TY - CHAP A1 - Rajan, Kohulan A1 - Zielesny, Achim A1 - Steinbeck, Christoph T1 - Also in Chemistry, Deep Learning Models Love Really Big Data T2 - Beilstein Bozen Symposium 2024 - AI in Chemistry and Biology: Evolution or Revolution?, Rüdesheim, Germany N2 - Inspired by the super-human performance of deep learning models in playing the game of Go after being presented with virtually unlimited training data, we looked into areas in chemistry where similar situations could be achieved. Encountering large amounts of training data in chemistry is still rare, so we turned to two areas where realistic training data can be fabricated in large quantities, namely a) the recognition of machine-readable structures from images of chemical diagrams and b) the conversion of IUPAC(-like) names into structures and vice versa. In this talk, we outline the challenges, technical implementation and results of this study. Optical Chemical Structure Recognition (OCSR): Vast amounts of chemical information remain hidden in the primary literature and have yet to be curated into open-access databases. To automate the process of extracting chemical structures from scientific papers, we developed the DECIMER.ai project. This open-source platform provides an integrated solution for identifying, segmenting, and recognising chemical structure depictions in scientific literature. DECIMER.ai comprises three main components: DECIMER-Segmentation, which utilises a Mask-RCNN model to detect and segment images of chemical structure depictions; DECIMER-Image Classifier EfficientNet-based classification model identifies which images contain chemical structures and DECIMER-Image Transformer which acts as an OCSR engine which combines an encoder-decoder model to convert the segmented chemical structure images into machine-readable formats, like the SMILES string. DECIMER.ai is data-driven, relying solely on the training data to make accurate predictions without hand-coded rules or assumptions. The latest model was trained with 127 million structures and 483 million depictions (4 different per structure) on Google TPU-V4 VMs Name to Structure Conversion: The conversion of structures to IUPAC(-like) or systematic names has been solved algorithmically or rule-based in satisfying ways. This fact, on the other side, provided us with an opportunity to generate a name-structure training pair at a very large scale to train a proof-of-concept transformer network and evaluate its performance. In this work, the largest model was trained using almost one billion SMILES strings. The Lexichem software utility from OpenEye was employed to generate the IUPAC names used in the training process. STOUT V2 was trained on Google TPU-V4 VMs. The model's accuracy was validated through one-to-one string matching, BLEU scores, and Tanimoto similarity calculations. To further verify the model's reliability, every IUPAC name generated by STOUT V2 was analysed for accuracy and retranslated using OPSIN, a widely used open-source software for converting IUPAC names to SMILES. This additional validation step confirmed the high fidelity of STOUT V2's translations. Y1 - 2024 ER - TY - JOUR A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Structure, Electronic Properties and NMR-Shielding of Cucurbit[n]urils JF - Journal of inclusion phenomena and macrocyclic chemistry Y1 - 2006 U6 - https://doi.org/10.1007/s10847-005-4602-2 SN - 0923-0750 VL - 54 IS - 1-2 SP - 85 EP - 88 ER - TY - CHAP A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Understanding the Cucurbit[6]uril-Spermine-Complex: Geometry and Electronic Interactions T2 - Konferenz: 1st German Conference of Chemoinformatics. 13.-15. November 2005 in Goslar Y1 - 2005 ER - TY - GEN A1 - Zielesny, Achim T1 - Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics [Softwarecode, Version 1.3.0.0] Y1 - 2019 UR - https://github.com/zielesny/Jdpd/releases/tag/1.3.0.0 ER - TY - CHAP A1 - Bänsch, Felix A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - Towards a comprehensive open computational support cycle for Molecular Fragment Dissipative Particle Dynamics (DPD) T2 - Konferenz: 15th German Conference on Cheminformatics GCC 2019, 3.-5. November 2019 in Mainz Y1 - 2019 ER - TY - GEN A1 - Zielesny, Achim T1 - Molecule Set Compensator [Softwarecode, Version 1.0] Y1 - 2020 UR - https://github.com/zielesny/MSC/releases/tag/1.0 ER - TY - JOUR A1 - Zielesny, Achim T1 - Chemistry Software Package ChemOffice Ultra 2005 JF - Journal of Chemical Information and Modeling Y1 - 2005 U6 - https://doi.org/10.1021/ci050273j SN - 1549-9596 VL - 45 IS - 5 SP - 1474 EP - 1477 ER - TY - CHAP A1 - Buschmann, Hans-Jürgen A1 - Wego, Andreas A1 - Zielesny, Achim A1 - Schollmeyer, Eckhard T1 - Structure, Electronic Properties and NMR-Shielding of Cucurbit[n]urils T2 - Konferenz: 1st German Conference of Chemoinformatics. 13.-15. November 2005 in Goslar Y1 - 2005 ER -