AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data

JOURNAL ARTICLE published 13 December 2023 in Journal of Cheminformatics

Research funded by Japan Agency for Medical Research and Development (JP22nk0101111)

Authors: Yugo Shimizu | Masateru Ohta | Shoichi Ishida | Kei Terayama | Masanori Osawa | Teruki Honma | Kazuyoshi Ikeda

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

JOURNAL ARTICLE published December 2009 in Journal of Cheminformatics

Authors: Tobias Lippert | Matthias Rarey

CLOUD – CeMM library of unique drugs

JOURNAL ARTICLE published December 2012 in Journal of Cheminformatics

Authors: Patrick Markt | Gerhard Dürnberger | Jacques Colinge | Stefan Kubicek

A molecule perturbation software library and its application to study the effects of molecular design constraints

JOURNAL ARTICLE published 26 September 2023 in Journal of Cheminformatics

Research funded by Fonds Wetenschappelijk Onderzoek (39461)

Authors: Alan Kerstjens | Hans De Winter

Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data

JOURNAL ARTICLE published December 2015 in Journal of Cheminformatics

Authors: Alex M Clark | Antony J Williams | Sean Ekins

GEN: highly efficient SMILES explorer using autodidactic generative examination networks

JOURNAL ARTICLE published December 2020 in Journal of Cheminformatics

Research funded by H2020 Marie Skłodowska-Curie Actions (676434)

Authors: Ruud van Deursen | Peter Ertl | Igor V. Tetko | Guillaume Godin

The semantics of Chemical Markup Language (CML): dictionaries and conventions

JOURNAL ARTICLE published December 2011 in Journal of Cheminformatics

Authors: Peter Murray-Rust | Joe A Townsend | Sam E Adams | Weerapong Phadungsukanan | Jens Thomas

TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine

JOURNAL ARTICLE published 31 December 2022 in Journal of Cheminformatics

Research funded by HKBU Strategic Development Fund project (SDF19 0402 P02) | National Key Research and Development Program of China (2021YFF1201400) | National Natural Science Foundation of China (22173118) | Hunan Provincial Science Fund for Distinguished Young Scholars (2021JJ10068) | the science and technology innovation Program of Hunan Province (2021RC4011) | Changsha Municipal Natural Science Foundation (kq2014144) | Changsha Science and Technology Bureau project (kq2001034)

Authors: Liu-Xia Zhang | Jie Dong | Hui Wei | Shao-Hua Shi | Ai-Ping Lu | Gui-Ming Deng | Dong-Sheng Cao

Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons

JOURNAL ARTICLE published December 2021 in Journal of Cheminformatics

Research funded by Empa (HALOSEARCH) | Swiss Polar Institute (DAAMAA)

Authors: Myriam Guillevic | Aurore Guillevic | Martin K. Vollmer | Paul Schlauri | Matthias Hill | Lukas Emmenegger | Stefan Reimann

Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis

JOURNAL ARTICLE published December 2012 in Journal of Cheminformatics

Authors: Sunghwan Kim | Evan E Bolton | Stephen H Bryant

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules

JOURNAL ARTICLE published December 2018 in Journal of Cheminformatics

Research funded by Russian Science Foundation (14-26-00094)

Authors: Ilia Korvigo | Maxim Holmatov | Anatolii Zaikovskii | Mikhail Skoblov

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

JOURNAL ARTICLE published December 2017 in Journal of Cheminformatics

Authors: Michael A. Skinnider | Chris A. Dejong | Brian C. Franczak | Paul D. McNicholas | Nathan A. Magarvey

KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images

JOURNAL ARTICLE published December 2019 in Journal of Cheminformatics

Research funded by Horizon 2020 (703543)

Authors: Isidro Cortés-Ciriano | Andreas Bender

Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy

JOURNAL ARTICLE published 7 March 2024 in Journal of Cheminformatics

Authors: Karina Jimenes-Vargas | Alejandro Pazos | Cristian R. Munteanu | Yunierkis Perez-Castillo | Eduardo Tejera

When drug discovery meets web search: Learning to Rank for ligand-based virtual screening

JOURNAL ARTICLE published December 2015 in Journal of Cheminformatics

Authors: Wei Zhang | Lijuan Ji | Yanan Chen | Kailin Tang | Haiping Wang | Ruixin Zhu | Wei Jia | Zhiwei Cao | Qi Liu

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal

JOURNAL ARTICLE published December 2020 in Journal of Cheminformatics

Research funded by Guangdong Province Key Area R&D Program (2019B010940001)

Authors: Pin Chen | Yu Wang | Hui Yan | Sen Gao | Zexin Xu | Yangzhong Li | Qing Mo | Junkang Huang | Jun Tao | GeChuanqi Pan | Jiahui Li | Yunfei Du

spyrmsd: symmetry-corrected RMSD calculations in Python

JOURNAL ARTICLE published December 2020 in Journal of Cheminformatics

Research funded by Biotechnology and Biological Sciences Research Council (BB/S50760X/1,BB/MO11224/1)

Authors: Rocco Meli | Philip C. Biggin

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

JOURNAL ARTICLE published December 2021 in Journal of Cheminformatics

Research funded by National Key R&D Program of China (2020YFB020003) | National Natural Science Foundation of China (61772566) | Introducing Innovative and Entrepreneurial Teams (2016ZT06D211) | Guangdong Key Field R&D Plan (2019B020228001,2018B010109006) | Guangzhou S&T Research Plan (202007030010)

Authors: Jianwen Chen | Shuangjia Zheng | Huiying Zhao | Yuedong Yang

A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19

JOURNAL ARTICLE published December 2020 in Journal of Cheminformatics

Authors: Alzbeta Tuerkova | Barbara Zdrazil

Structure-based, deep-learning models for protein-ligand binding affinity prediction

JOURNAL ARTICLE published 3 January 2024 in Journal of Cheminformatics

Research funded by National Natural Science Foundation of China (62203304,62176160,62376162) | Basic and Applied Basic Research Foundation of Guangdong Province (2022A1515010791)

Authors: Debby D. Wang | Wenhui Wu | Ran Wang