Iterative Rank based Methods for Clustering. - Sören W. Perrey; Heinrich Brinck; Achim Zielesny (CSB, 2003)

Chemistry Software Package ChemOffice Ultra 2005. - Achim Zielesny (J. Chem. Inf. Model., 2005)

CDK-Taverna: an open workflow environment for cheminformatics. - Thomas Kuhn; Egon L. Willighagen; Achim Zielesny; Christoph Steinbeck (BMC Bioinform., 2010)

Molecular fragments chemoinformatics. - Hubert Kuhn; Stefan Neumann 001; Christoph Steinbeck; Carsten Wittekindt; Achim Zielesny (J. Cheminformatics, 2010)

New developments on the cheminformatics open workflow environment CDK-Taverna. - Andreas Truszkowski; Kalai Vanii Jayaseelan; Stefan Neumann 001; Egon L. Willighagen; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2011)

CDK-Taverna 2.0: migration and enhancements of an open-source pipelining solution. - Andreas Truszkowski; Stefan Neumann 001; Achim Zielesny; Egon L. Willighagen; Christoph Steinbeck (J. Cheminformatics, 2011)

From Curve Fitting to Machine Learning - An Illustrative Guide to Scientific Data Analysis and Computational Intelligence - Achim Zielesny (Springer, 2011)

Adsorption of amino acids on MFI-type zeolite: DFT calculations and experimental results. - Kai Stueckenschneider; Achim Zielesny; Gerhard Schembecker (J. Cheminformatics, 2012)

Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD). - Andreas Truszkowski; Annamaria Fiethen; Hubert Kuhn; Achim Zielesny; Matthias Epple (J. Cheminformatics, 2013)

A molecular fragment cheminformatics roadmap for mesoscopic simulation. - Andreas Truszkowski; Mirco Daniel; Hubert Kuhn; Stefan Neumann 001; Christoph Steinbeck; Achim Zielesny; Matthias Epple (J. Cheminformatics, 2014)

Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants. - Andreas Truszkowski; Annamaria Fiethen; Hubert Kuhn; Thomas Wiebringhaus; Achim Zielesny; Matthias Epple (J. Cheminformatics, 2014)

Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics. - Andreas Truszkowski; Karina van den Broek; Hubert Kuhn; Achim Zielesny; Matthias Epple (J. Chem. Inf. Model., 2015)

From Curve Fitting to Machine Learning - An Illustrative Guide to Scientific Data Analysis and Computational Intelligence, Second Edition - Achim Zielesny (Springer, 2016)

SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation. - Karina van den Broek; Mirco Daniel; Matthias Epple; Hubert Kuhn; Jonas Schaub; Achim Zielesny (J. Cheminformatics, 2018)

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics. - Karina van den Broek; Hubert Kuhn; Achim Zielesny (J. Cheminformatics, 2018)

ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK). - Sebastian Fritsch; Stefan Neumann 001; Jonas Schaub; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2019)

MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation. - Karina van den Broek; Mirco Daniel; Matthias Epple; Jan-Mathis Hein; Hubert Kuhn; Stefan Neumann 001; Andreas Truszkowski; Achim Zielesny (J. Cheminformatics, 2020)

A review of optical chemical structure recognition tools. - Kohulan Rajan; Henning Otto Brinkhaus; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2020)

DECIMER: towards deep learning for chemical image recognition. - Kohulan Rajan; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2020)

Too sweet: cheminformatics for deglycosylation in natural products. - Jonas Schaub; Achim Zielesny; Christoph Steinbeck; Maria Sorokina (J. Cheminformatics, 2020)

DECIMER-Segmentation: Automated extraction of chemical structure depictions from scientific literature. - Kohulan Rajan; Henning Otto Brinkhaus; Maria Sorokina; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2021)

Molecule Set Comparator (MSC): a CDK-based open rich-client tool for molecule set similarity evaluations. - Kohulan Rajan; Jan-Mathis Hein; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2021)

STOUT: SMILES to IUPAC names using neural machine translation. - Kohulan Rajan; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2021)

DECIMER 1.0: deep learning for chemical image recognition using transformers. - Kohulan Rajan; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2021)

Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation. - Karina van den Broek; Matthias Epple; Lisa Sophie Kersten; Hubert Kuhn; Achim Zielesny (J. Chem. Inf. Model., 2021)

RanDepict: Random chemical structure depiction generator. - Henning Otto Brinkhaus; Kohulan Rajan; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2022)

DECIMER - hand-drawn molecule images dataset. - Henning Otto Brinkhaus; Achim Zielesny; Christoph Steinbeck; Kohulan Rajan (J. Cheminformatics, 2022)

Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). - Jonas Schaub; Julian Zander; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2022)

MORTAR: a rich client application for in silico molecule fragmentation. - Felix Bänsch; Jonas Schaub; Betül Sevindik; Samuel Behr; Julian Zander; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2023)

Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C10E4/water mixture with lamellar bilayer formation. - Felix Bänsch; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2023)

An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package. - Felix Bänsch; Mirco Daniel; Harald Lanig; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2024)

Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture. - Kohulan Rajan; Henning Otto Brinkhaus; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2024)

STOUT V2.0: SMILES to IUPAC name conversion using transformer models. - Kohulan Rajan; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2024)

PySSA for Windows: End-User Protein Structure Prediction and Visual Analysis with ColabFold and PyMOL. - Hannah Kullik; Martin Urban; Jonas Schaub; Angelika Loidl-Stahlhofen; Achim Zielesny (J. Chem. Inf. Model., 2025)