Works in Journal of Cheminformatics, 2025, Vol 17, Issue 1

Results: 97

Correction: Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach.

Published in:

2025

By:

Hammad, Raheel;
Mondal, Sownyak

Publication type:

Correction Notice

The development of the generative adversarial supporting vector machine for molecular property generation.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01052-x

By:

Lu, Qing

Publication type:

Article

Implementation of an open chemistry knowledge base with a Semantic Wiki.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01037-w

By:

Neidiger, Charlotte;
Saier, Tarek;
Kühn, Kai;
Larignon, Victor;
Färber, Michael;
Bizzarri, Claudia;
Šimek Tosino, Helena;
Holzhauer, Laura;
Erdmann, Michael;
Nguyen, An;
Harvey, Dean;
Tremouilhac, Pierre;
Kramer, Claudia;
Hansch, Daniel;
Schönle, Fabian;
Alpin, Jana;
Hartmann, Maximilian;
Wagner, Jérome;
Jung, Nicole;
Bräse, Stefan

Publication type:

Article

Shinyscreen: mass spectrometry data inspection and quality checking utility.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01044-x

By:

Kondić, Todor;
Elapavalore, Anjana;
Krier, Jessy;
Lai, Adelene;
Taha, Hiba Mohammed;
Narayanan, Mira;
Schymanski, Emma L.

Publication type:

Article

Crossover operators for molecular graphs with an application to virtual drug screening.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00958-w

By:

Domschke, Nico;
Schmidt, Bruno J.;
Gatter, Thomas;
Golnik, Richard;
Eisenhuth, Paul;
Liessmann, Fabian;
Meiler, Jens;
Stadler, Peter F.

Publication type:

Article

NanoBinder: a machine learning assisted nanobody binding prediction tool using Rosetta energy scores.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01040-1

By:

Shrestha, Palistha;
Talwar, Chandana S.;
Kandel, Jeevan;
Park, Kwang-Hyun;
Chong, Kil To;
Woo, Eui-Jeon;
Tayara, Hilal

Publication type:

Article

Advancements in thermochemical predictions: a multi-output thermodynamics-informed neural network approach.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01033-0

By:

Hammad, Raheel;
Mondal, Sownyak

Publication type:

Article

UMAP-based clustering split for rigorous evaluation of AI models for virtual screening on cancer cell lines.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01039-8

By:

Guo, Qianrong;
Hernandez-Hernandez, Saiveth;
Ballester, Pedro J.

Publication type:

Article

A 3D generation framework using diffusion model and reinforcement learning to generate multi-target compounds with desired properties.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01035-y

By:

Yuan, Yongna;
Pan, Xiaohang;
Li, Xiaohong;
Zhang, Ruisheng;
Su, Wei

Publication type:

Article

RLSuccSite: succinylation sites prediction based on reinforcement learning dynamic with balanced reward mechanism and three-peaks enhanced method for physicochemical property scores.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01034-z

By:

Zhu, Lun;
Zhang, Qingchao;
Yang, Sen

Publication type:

Article

Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01030-3

By:

Astero, Maryam;
Rousu, Juho

Publication type:

Article

Enhancing molecular property prediction with quantized GNN models.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00989-3

By:

Rasool, Areen;
Ul Rahman, Jamshaid;
Uwitije, Rongin

Publication type:

Article

Context-dependent similarity searching for small molecular fragments.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01032-1

By:

Yoshimori, Atsushi;
Bajorath, Jürgen

Publication type:

Article

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01031-2

By:

Peets, Pilleriin;
Litos, Aristeidis;
Dührkop, Kai;
Garza, Daniel R.;
van der Hooft, Justin J. J.;
Böcker, Sebastian;
Dutilh, Bas E.

Publication type:

Article

Surfactant representation using COSMO screened charge density for adsorption isotherm prediction using Physics-Informed Neural Network (PINN).

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01027-y

By:

Alimin, Achmad Anggawirya;
Srasamran, Kattariya;
Yuenyong, Wanutchaya;
Charoensaeng, Ampira;
Shiau, Bor-Jier;
Suriyapraphadilok, Uthaiporn

Publication type:

Article

ELNdataBridge: facilitating data exchange and collaboration by linking Electronic Lab Notebooks via API.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01024-1

By:

Starman, Martin;
Kirchner, Fabian;
Held, Martin;
Eschke, Catriona;
Sahim, Sayed-Ahmad;
Willumeit-Römer, Regine;
Jung, Nicole;
Bräse, Stefan

Publication type:

Article

Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01022-3

By:

Martínez León, Alejandro;
Ries, Benjamin;
Hub, Jochen S.;
Magarkar, Aniket

Publication type:

Article

Benchmarking molecular conformer augmentation with context-enriched training: graph-based transformer versus GNN models.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01004-5

By:

Valsecchi, Cecile;
Arjona-Medina, Jose A.;
Dyubankova, Natalia;
Nugmanov, Ramil

Publication type:

Article

Machine learning-driven generation and screening of potential ionic liquids for cellulose dissolution.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01018-z

By:

Qu, Mengyang;
Sharma, Gyanendra;
Wada, Naoki;
Ikebata, Hisaki;
Matsunami, Shigeyuki;
Takahashi, Kenji

Publication type:

Article

A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01017-0

By:

Li, Qingliang;
Kim, Sunghwan;
Zaslavsky, Leonid;
Cheng, Tiejun;
Yu, Bo;
Bolton, Evan E.

Publication type:

Article

Advantages of two quantum programming platforms in quantum computing and quantum chemistry.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01026-z

By:

Wang, Pei-Hua;
Wu, Wei-Yeh;
Lee, Che-Yu;
Hong, Jia-Cheng;
Tseng, Yufeng Jane

Publication type:

Article

Assessing interaction recovery of predicted protein-ligand poses.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01011-6

By:

Errington, David;
Schneider, Constantin;
Bouysset, Cédric;
Dreyer, Frédéric A.

Publication type:

Article

Addressing standardization and semantics in an electronic lab notebook for multidisciplinary use: LabIMotion.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01021-4

By:

Lin, Chia-Lin;
Huang, Pei-Chi;
Wöll, Christof;
Théato, Patrick;
Kübel, Christian;
Pilz, Lena;
Jung, Nicole;
Bräse, Stefan

Publication type:

Article

Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01012-5

By:

Ha, Sumin;
Bang, Dongmin;
Kim, Sun

Publication type:

Article

Generating diversity and securing completeness in algorithmic retrosynthesis.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00981-x

By:

Mrugalla, Florian;
Franz, Christopher;
Alber, Yannic;
Mogk, Georg;
Villalba, Martín;
Mrziglod, Thomas;
Schewior, Kevin

Publication type:

Article

Generalizable, fast, and accurate DeepQSPR with fastprop.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01013-4

By:

Burns, Jackson W.;
Green, William H.

Publication type:

Article

The published role of artificial intelligence in drug discovery and development: a bibliometric and social network analysis from 1990 to 2023.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00988-4

By:

Koçak, Murat;
Akçalı, Zafer

Publication type:

Article

Application of 3D atom pair map in an attention model for enhanced drug virtual screening.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01023-2

By:

Ryu, Gina;
Kim, Wankyu

Publication type:

Article

Predicting inhibitors of OATP1B1 via heterogeneous OATP-ligand interaction graph neural network (HOLIgraph).

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01020-5

By:

Mardikoraem, Mehrsa;
Eaves, Joelle N.;
Belecciu, Theodore;
Pascual, Nathaniel;
Aljets, Alexander;
Hagenbuch, Bruno;
Shapiro, Erik M.;
Orlando, Benjamin J.;
Woldring, Daniel R.

Publication type:

Article

Prediction of blood–brain barrier and Caco-2 permeability through the Enalos Cloud Platform: combining contrastive learning and atom-attention message passing neural networks.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01007-2

By:

Koutroumpa, Nikoletta-Maria;
Tsoumanis, Andreas;
Sarimveis, Haralambos;
Lynch, Iseult;
Melagraki, Georgia;
Afantitis, Antreas

Publication type:

Article

Leveraging AI to explore structural contexts of post-translational modifications in drug binding.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01019-y

By:

Medvedev, Kirill E.;
Schaeffer, R. Dustin;
Grishin, Nick V.

Publication type:

Article

Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01015-2

By:

Permadi, Elpri Eka;
Watanabe, Reiko;
Mizuguchi, Kenji

Publication type:

Article

E-GuARD: expert-guided augmentation for the robust detection of compounds interfering with biological assays.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01014-3

By:

Palmacci, Vincenzo;
Nahal, Yasmine;
Welsch, Matthias;
Engkvist, Ola;
Kaski, Samuel;
Kirchmair, Johannes

Publication type:

Article

LAGNet: better electron density prediction for LCAO-based data and drug-like substances.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01010-7

By:

Ushenin, Konstantin;
Khrabrov, Kuzma;
Tsypin, Artem;
Ber, Anton;
Rumiantsev, Egor;
Kadurin, Artur

Publication type:

Article

Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01009-0

By:

Szwarc, Sarah;
Rutz, Adriano;
Lee, Kyungha;
Mejri, Yassine;
Bonnet, Olivier;
Hazni, Hazrina;
Jagora, Adrien;
Mbeng Obame, Rany B.;
Noh, Jin Kyoung;
Otogo N'Nang, Elvis;
Alaribe, Stephenie C.;
Awang, Khalijah;
Bernadat, Guillaume;
Choi, Young Hae;
Courdavault, Vincent;
Frederich, Michel;
Gaslonde, Thomas;
Huber, Florian;
Kam, Toh-Seok;
Low, Yun Yee

Publication type:

Article

SMILES all around: structure to SMILES conversion for transition metal complexes.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01008-1

By:

Rasmussen, Maria H.;
Strandgaard, Magnus;
Seumer, Julius;
Hemmingsen, Laura K.;
Frei, Angelo;
Balcells, David;
Jensen, Jan H.

Publication type:

Article

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01005-4

By:

Halfar, Radek;
Damborský, Jiří;
Marques, Sérgio M.;
Martinovič, Jan

Publication type:

Article

Visualising lead optimisation series using reduced graphs.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01002-7

By:

Stacey, Jessica;
Canault, Baptiste;
Pickett, Stephen D.;
Gillet, Valerie J.

Publication type:

Article

Prediction of the water solubility by a graph convolutional-based neural network on a highly curated dataset.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01000-9

By:

Ulrich, Nadin;
Voigt, Karsten;
Kudria, Anton;
Böhme, Alexander;
Ebert, Ralf-Uwe

Publication type:

Article

High-throughput screening data generation, scoring and FAIRification: a case study on nanomaterials.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01001-8

By:

Tancheva, Gergana;
Hongisto, Vesa;
Patyra, Konrad;
Iliev, Luchesar;
Kochev, Nikolay;
Nymark, Penny;
Kohonen, Pekka;
Jeliazkova, Nina;
Grafström, Roland

Publication type:

Article

GESim: ultrafast graph-based molecular similarity calculation via von Neumann graph entropy.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01003-6

By:

Shiokawa, Hiroaki;
Ishida, Shoichi;
Terayama, Kei

Publication type:

Article

Learning motif features and topological structure of molecules for metabolic pathway prediction.

Published in:

2025

By:

Hu, Jianguo;
Zhang, Yiqing;
Xie, Jinxin;
Yuan, Zhen;
Yin, Zhangxiang;
Shi, Shanshan;
Li, Honglin;
Li, Shiliang

Publication type:

Editorial

Activity cliff-aware reinforcement learning for de novo drug design.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-01006-3

By:

Hu, Xiuyuan;
Liu, Guoqing;
Zhao, Yang;
Zhang, Hao

Publication type:

Article

Molecular property prediction using pretrained-BERT and Bayesian active learning: a data-efficient approach to drug design.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00986-6

By:

Masood, Muhammad Arslan;
Kaski, Samuel;
Cui, Tianyu

Publication type:

Article

The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00977-7

By:

Rihon, Jérôme;
Reynders, Sten;
Bernardes Pinheiro, Vitor;
Lescrinier, Eveline

Publication type:

Article

Integrating QSAR modelling with reinforcement learning for Syk inhibitor discovery.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00998-2

By:

Zavadskaya, Maria;
Orlova, Anastasia;
Dmitrenko, Andrei;
Vinogradov, Vladimir

Publication type:

Article

InertDB as a generative AI-expanded resource of biologically inactive small molecules from PubChem.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00999-1

By:

An, Seungchan;
Lee, Yeonjin;
Gong, Junpyo;
Hwang, Seokyoung;
Park, In Guk;
Cho, Jayhyun;
Lee, Min Ju;
Kim, Minkyu;
Kang, Yun Pyo;
Noh, Minsoo

Publication type:

Article

An interpretable deep geometric learning model to predict the effects of mutations on protein–protein interactions using large-scale protein language model.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00979-5

By:

Zhang, Caiya;
Sun, Yan;
Hu, Pingzhao

Publication type:

Article

Unveiling polyphenol-protein interactions: a comprehensive computational analysis.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00997-3

By:

Lešnik, Samo;
Jukić, Marko;
Bren, Urban

Publication type:

Article

HepatoToxicity Portal (HTP): an integrated database of drug-induced hepatotoxicity knowledgebase and graph neural network-based prediction model.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00992-8

By:

Han, Jiyeon;
Zhung, Wonho;
Jang, Insoo;
Lee, Joongwon;
Kang, Min Ji;
Lee, Timothy Dain;
Kwack, Seung Jun;
Kim, Kyu-Bong;
Hwang, Daehee;
Lee, Byungwook;
Kim, Hyung Sik;
Kim, Woo Youn;
Lee, Sanghyuk

Publication type:

Article