J. Cheminformatics

Publications

volume 16, number 1, 2024

Tsuyoshi Esaki, Tomoki Yonezawa, Kazuyoshi Ikeda
A new workflow for the effective curation of membrane permeability data from open ADME information. J. Cheminformatics 16 (1) (2024)
Markus Orsi, Jean-Louis Reymond
One chiral fingerprint to find them all. J. Cheminformatics 16 (1) (2024)
David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer. J. Cheminformatics 16 (1) (2024)
Maarten R. Dobbelaere, István Lengyel, Christian V. Stevens, Kevin M. Van Geem
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices. J. Cheminformatics 16 (1) (2024)
Yaxin Gu, Yimeng Wang, Keyun Zhu, Weihua Li, Guixia Liu, Yun Tang
DBPP-Predictor: a novel strategy for prediction of chemical drug-likeness based on property profiles. J. Cheminformatics 16 (1) (2024)
Jeaphianne P. M. van Rijn, Marvin Martens, Ammar Ammar, Mihaela Roxana Cimpan, Valerie Fessard, Peter Hoet, Nina Jeliazkova, Sivakumar Murugadoss, Ivana Vinkovic Vrcek, Egon L. Willighagen
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials. J. Cheminformatics 16 (1) (2024)
Zhijiang Yang, Tengxin Huang, Li Pan, Jingjing Wang, Liangliang Wang, Junjie Ding, Junhua Xiao
QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning. J. Cheminformatics 16 (1) (2024)
Alex K. Chew, Matthew Sender, Zachary Kaplan, Anand Chandrasekaran, Jackson Chief Elk, Andrea R. Browning, H. Shaun Kwak, Mathew D. Halls, Mohammad Atif Faiz Afzal
Advancing material property prediction: using physics-informed machine learning models for viscosity. J. Cheminformatics 16 (1) (2024)
Paula Carracedo-Reboredo, Eider Aranzamendi, Shan He, Sonia Arrasate, Cristian R. Munteanu, Carlos Fernandez-Lozano, Nuria Sotomayor, Esther Lete, Humberto González Díaz
MATEO: intermolecular α-amidoalkylation theoretical enantioselectivity optimization. Online tool for selection and design of chiral catalysts and products. J. Cheminformatics 16 (1) (2024)
Tinghao Zhang, Shaohua Sun, Runzhou Wang, Ting Li, Bicheng Gan, Yuezhou Zhang
BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. J. Cheminformatics 16 (1) (2024)
Jeevan Kandel, Palistha Shrestha, Hilal Tayara, Kil To Chong
PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction. J. Cheminformatics 16 (1) (2024)
Sadettin Y. Ugurlu, David W. McDonald, Huangshu Lei, Alan M. Jones, Shu Li, Henry H. Y. Tong, Mark S. Butler, Shan He
Cobdock: an accurate and practical machine learning-based consensus blind docking method. J. Cheminformatics 16 (1) (2024)
Maryam Astero, Juho Rousu
Learning symmetry-aware atom mapping in chemical reactions through deep graph matching. J. Cheminformatics 16 (1) (2024)
Yufang Zhang, Jiayi Li, Shenggeng Lin, Jianwei Zhao, Yi Xiong, Dong-Qing Wei
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model. J. Cheminformatics 16 (1) (2024)
Lung-Yi Chen, Yi-Pei Li
AutoTemplate: enhancing chemical reaction datasets for machine learning applications in organic chemistry. J. Cheminformatics 16 (1) (2024)
Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma Schymanski
InChI isotopologue and isotopomer specifications. J. Cheminformatics 16 (1) (2024)
Christina Humer, Rachel Nicholls, Henry Heberle, Moritz Heckmann, Michael Pühringer, Thomas Wolf, Maximilian Lübbesmeyer, Julian Heinrich, Julius Hillenbrand, Giulio Volpin, Marc Streit
CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space. J. Cheminformatics 16 (1) (2024)
Adrià Cereto-Massagué, Santiago Garcia-Vallvé, Gerard Pujadas
Correction: DecoyFinder, a tool for finding decoy molecules. J. Cheminformatics 16 (1) (2024)
Niklas Dobberstein, Astrid Maass, Jan Hamaekers
Llamol: a dynamic multi-conditional generative transformer for de novo molecular design. J. Cheminformatics 16 (1) (2024)
Jiangxia Wu, Yihao Chen, Jingxing Wu, Duancheng Zhao, Jindi Huang, MuJie Lin, Ling Wang
Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors. J. Cheminformatics 16 (1) (2024)
Anuj Gahlawat, Anjali Singh, Hardeep Sandhu, Prabha Garg
CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm. J. Cheminformatics 16 (1) (2024)
Barbara Zdrazil, Rajarshi Guha, Karina Martínez-Mayorga, Nina Jeliazkova
Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics' Scientific Contribution Statement. J. Cheminformatics 16 (1) (2024)
Alexander S. Behr, Hendrik Borgelt, Norbert Kockmann
Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management. J. Cheminformatics 16 (1) (2024)
Sadjad Fakouri Baygi, Dinesh Kumar Barupal
IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra. J. Cheminformatics 16 (1) (2024)
Lung-Yi Chen, Yi-Pei Li
Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions. J. Cheminformatics 16 (1) (2024)
Matteo Krüger, Ashmi Mishra, Peter Spichtinger, Ulrich Pöschl, Thomas Berkemeier
A numerical compass for experiment design in chemical kinetics and molecular property estimation. J. Cheminformatics 16 (1) (2024)
Lukasz Maziarka, Dawid Majchrowski, Tomasz Danel, Piotr Gainski, Jacek Tabor, Igor T. Podolak, Pawel M. Morkisz, Stanislaw Jastrzebski
Relative molecule self-attention transformer. J. Cheminformatics 16 (1) (2024)
Lingling Shen, Jian Fang, Lulu Liu, Fei Yang, Jeremy L. Jenkins, Peter S. Kutchukian, He Wang
Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery. J. Cheminformatics 16 (1) (2024)
Kamel Mansouri, José T. Moreira-Filho, Charles N. Lowe, Nathaniel Charest, Todd Martin, Valery Tkachenko, Richard S. Judson, Mike Conway, Nicole C. Kleinstreuer, Antony J. Williams
Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling. J. Cheminformatics 16 (1) (2024)
Wenjia Qian, Xiaorui Wang, Yu Kang, Peichen Pan, Tingjun Hou, Chang-Yu Hsieh
A general model for predicting enzyme functions based on enzymatic reactions. J. Cheminformatics 16 (1) (2024)
Klaudia Caba, Viet-Khoa Tran-Nguyen, Taufiq Rahman, Pedro J. Ballester
Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors. J. Cheminformatics 16 (1) (2024)
Zhijiang Yang, Tengxin Huang, Li Pan, Jingjing Wang, Liangliang Wang, Junjie Ding, Junhua Xiao
Correction: QuanDB: a quantum chemical property database towards enhancing 3D molecular representation learning. J. Cheminformatics 16 (1) (2024)
Marie Oestreich, Iva Ewert, Matthias Becker
Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability. J. Cheminformatics 16 (1) (2024)
Julia Rahman, M. A. Hakim Newton, Mohammed Eunus Ali, Abdul Sattar
Distance plus attention for binding affinity prediction. J. Cheminformatics 16 (1) (2024)
Zihui Huang, Liqiang He, Yuhang Yang, Andi Li, Zhiwen Zhang, Siwei Wu, Yang Wang, Yan He, Xujie Liu
Application of machine reading comprehension techniques for named entity recognition in materials science. J. Cheminformatics 16 (1) (2024)
Satnam Singh, Gina Zeh, Jessica Freiherr, Thilo Bauer, Isik Türkmen, Andreas Grasskamp
Classification of substances by health hazard using deep neural networks and molecular electron densities. J. Cheminformatics 16 (1) (2024)
Said Moshawih, Zhen Hui Bu, Hui Poh Goh, Nurolaini Kifli, Lam Hong Lee, Khang Wen Goh, Chiau Ming Long
Consensus holistic virtual screening for drug discovery: a novel machine learning model approach. J. Cheminformatics 16 (1) (2024)
Staffan Arvidsson McShane, Ulf Norinder, Jonathan Alvarsson, Ernst Ahlberg, Lars Carlsson, Ola Spjuth
CPSign: conformal prediction for cheminformatics modeling. J. Cheminformatics 16 (1) (2024)
Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. J. Cheminformatics 16 (1) (2024)
Joseph Heeley, Samuel Boobier, Jonathan D. Hirst
Solvent flashcards: a visualisation tool for sustainable chemistry. J. Cheminformatics 16 (1) (2024)
Jongmin Han, Youngchun Kwon, Youn-Suk Choi, Seokho Kang
Improving chemical reaction yield prediction using pre-trained graph neural networks. J. Cheminformatics 16 (1) (2024)
Hengwei Chen, Jürgen Bajorath
Generative design of compounds with desired potency from target protein sequences using a multimodal biochemical language model. J. Cheminformatics 16 (1) (2024)
Derek Long, Liam Eade, Matthew P. Sullivan, Katharina Dost, Samuel M. Meier-Menches, David C. Goldstone, Christian G. Hartinger, Jörg S. Wicker, Katerina Taskova
AdductHunter: identifying protein-metal complex adducts in mass spectra. J. Cheminformatics 16 (1) (2024)
Jonghyun Lee, Dae Won Jun, Ildae Song, Yun Kim
DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning. J. Cheminformatics 16 (1) (2024)
Bowen Tang, Zhangming Niu, Xiaofeng Wang, Junjie Huang, Chao Ma, Jing Peng, Yinghui Jiang, Ruiquan Ge, Hongyu Hu, Luhao Lin, Guang Yang
Automated molecular structure segmentation from documents using ChemSAM. J. Cheminformatics 16 (1) (2024)
Zachary A. Rollins, Alan C. Cheng, Essam Metwally
MolPROP: Molecular Property prediction with multimodal language and graph fusion. J. Cheminformatics 16 (1) (2024)
Runhan Shi, Gufeng Yu, Xiaohong Huo, Yang Yang
Prediction of chemical reaction yields with large-scale multi-view pre-training. J. Cheminformatics 16 (1) (2024)
Wei-Cheng Huang, Wei-Ting Lin, Ming-Shiu Hung, Jinq-Chyi Lee, Chun-Wei Tung
Decrypting orphan GPCR drug discovery via multitask learning. J. Cheminformatics 16 (1) (2024)
Soyeon Lee, Sunyong Yoo
InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism. J. Cheminformatics 16 (1) (2024)
Debby D. Wang, Wenhui Wu, Ran Wang
Structure-based, deep-learning models for protein-ligand binding affinity prediction. J. Cheminformatics 16 (1) (2024)