Works matching IS 17582946 AND DT 2024 AND VI 16 AND IP 1

Results: 135

Milestones in chemoinformatics: global view of the field.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00922-0

By:

Bajorath, Jürgen

Publication type:

Article

StreaMD: the toolkit for high-throughput molecular dynamics simulations.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00918-w

By:

Ivanova, Aleksandra;
Mokshyna, Olena;
Polishchuk, Pavel

Publication type:

Article

Quantitative structure–activity relationships of chemical bioactivity toward proteins associated with molecular initiating events of organ-specific toxicity.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00917-x

By:

Gadaleta, Domenico;
Garcia de Lomana, Marina;
Serrano-Candelas, Eva;
Ortega-Vallbona, Rita;
Gozalbes, Rafael;
Roncaglioni, Alessandra;
Benfenati, Emilio

Publication type:

Article

Searching chemical databases in the pre-history of cheminformatics.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00919-9

By:

Willett, Peter

Publication type:

Article

Accurate prediction of protein–ligand interactions by combining physical energy functions and graph-neural networks.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00912-2

By:

Hong, Yiyu;
Ha, Junsu;
Sim, Jaemin;
Lim, Chae Jo;
Oh, Kwang-Seok;
Chandrasekaran, Ramakrishnan;
Kim, Bomin;
Choi, Jieun;
Ko, Junsu;
Shin, Woong-Hee;
Lee, Juyong

Publication type:

Article

GTransCYPs: an improved graph transformer neural network with attention pooling for reliably predicting CYP450 inhibitors.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00915-z

By:

Zonyfar, Candra;
Ngnamsie Njimbouom, Soualihou;
Mosalla, Sophia;
Kim, Jeong-Dong

Publication type:

Article

A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00913-1

By:

Abdollahi, Sina;
Schaub, Darius P.;
Barroso, Madalena;
Laubach, Nora C.;
Hutwelker, Wiebke;
Panzer, Ulf;
Gersting, S.øren W.;
Bonn, Stefan

Publication type:

Article

Towards the prediction of drug solubility in binary solvent mixtures at various temperatures using machine learning.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00911-3

By:

Bao, Zeqing;
Tom, Gary;
Cheng, Austin;
Watchorn, Jeffrey;
Aspuru-Guzik, Alán;
Allen, Christine

Publication type:

Article

Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00904-2

By:

García-Ortegón, Miguel;
Seal, Srijit;
Rasmussen, Carl;
Bender, Andreas;
Bacallado, Sergio

Publication type:

Article

MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00882-5

By:

Ugurlu, Sadettin Y.;
McDonald, David;
He, Shan

Publication type:

Article

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme–ligand complexes.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00907-z

By:

Vavra, O.;
Tyzack, J.;
Haddadi, F.;
Stourac, J.;
Damborsky, J.;
Mazurenko, S.;
Thornton, J. M.;
Bednar, D.

Publication type:

Article

Bitter peptide prediction using graph neural networks.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00909-x

By:

Srivastava, Prashant;
Steuer, Alexandra;
Ferri, Francesco;
Nicoli, Alessandro;
Schultz, Kristian;
Bej, Saptarshi;
Di Pizio, Antonella;
Wolkenhauer, Olaf

Publication type:

Article

Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00906-0

By:

Sharma, Sejal;
Feng, Liping;
Boonpattrawong, Nicha;
Kapur, Arvinder;
Barroilhet, Lisa;
Patankar, Manish S.;
Ericksen, Spencer S.

Publication type:

Article

Insights into predicting small molecule retention times in liquid chromatography using deep learning.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00905-1

By:

Liu, Yuting;
Yoshizawa, Akiyasu C.;
Ling, Yiwei;
Okuda, Shujiro

Publication type:

Article

A multi-view feature representation for predicting drugs combination synergy based on ensemble and multi-task attention models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00903-3

By:

Monem, Samar;
Hassanien, Aboul Ella;
Abdel-Hamid, Alaa H.

Publication type:

Article

Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00902-4

By:

Torres, Luis H. M.;
Arrais, Joel P.;
Ribeiro, Bernardete

Publication type:

Article

Computer-aided pattern scoring (C@PS): a novel cheminformatic workflow to predict ligands with rare modes-of-action.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00901-5

By:

Stefan, Sven Marcel;
Stefan, Katja;
Namasivayam, Vigneshwaran

Publication type:

Article

RAIChU: automating the visualisation of natural product biosynthesis.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00898-x

By:

Terlouw, Barbara R.;
Biermann, Friederike;
Vromans, Sophie P. J. M.;
Zamani, Elham;
Helfrich, Eric J. N.;
Medema, Marnix H.

Publication type:

Article

EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00893-2

By:

Fan, Zhiguang;
Yang, Yuedong;
Xu, Mingyuan;
Chen, Hongming

Publication type:

Article

Evaluating the generalizability of graph neural networks for predicting collision cross section.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00899-w

By:

Engler Hart, Chloe;
Preto, António José;
Chanana, Shaurya;
Healey, David;
Kind, Tobias;
Domingo-Fernández, Daniel

Publication type:

Article

BuildAMol: a versatile Python toolkit for fragment-based molecular design.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00900-6

By:

Kleinschmidt, Noah;
Lemmin, Thomas

Publication type:

Article

Deep learning of multimodal networks with topological regularization for drug repositioning.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00897-y

By:

Ohnuki, Yuto;
Akiyama, Manato;
Sakakibara, Yasubumi

Publication type:

Article

Automatic molecular fragmentation by evolutionary optimisation.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00896-z

By:

Yu, Fiona C. Y.;
Vallejo, Jorge L. Gálvez;
Barca, Giuseppe M. J.

Publication type:

Article

Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00894-1

By:

Moreira-Filho, José T.;
Ranganath, Dhruv;
Conway, Mike;
Schmitt, Charles;
Kleinstreuer, Nicole;
Mansouri, Kamel

Publication type:

Article

Metis: a python-based user interface to collect expert feedback for generative chemistry models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00892-3

By:

Menke, Janosch;
Nahal, Yasmine;
Bjerrum, Esben Jannik;
Kabeshov, Mikhail;
Kaski, Samuel;
Engkvist, Ola

Publication type:

Article

Geometric deep learning for molecular property predictions with chemical accuracy across chemical space.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00895-0

By:

Dobbelaere, Maarten R.;
Lengyel, István;
Stevens, Christian V.;
Van Geem, Kevin M.

Publication type:

Article

MolCompass: multi-tool for the navigation in chemical space and visual validation of QSAR/QSPR models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00888-z

By:

Sosnin, Sergey

Publication type:

Article

Building shape-focused pharmacophore models for effective docking screening.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00857-6

By:

Moyano-Gómez, Paola;
Lehtonen, Jukka V.;
Pentikäinen, Olli T.;
Postila, Pekka A.

Publication type:

Article

An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00890-5

By:

Bänsch, Felix;
Daniel, Mirco;
Lanig, Harald;
Steinbeck, Christoph;
Zielesny, Achim

Publication type:

Article

Evaluation of reinforcement learning in transformer-based molecular design.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00887-0

By:

He, Jiazhen;
Tibo, Alessandro;
Janet, Jon Paul;
Nittinger, Eva;
Tyrchan, Christian;
Czechtizky, Werngard;
Engkvist, Ola

Publication type:

Article

Hamiltonian diversity: effectively measuring molecular diversity by shortest Hamiltonian circuits.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00883-4

By:

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

Publication type:

Article

Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00881-6

By:

Hafner, Jasmin;
Lorsbach, Tim;
Schmidt, Sebastian;
Brydon, Liam;
Dost, Katharina;
Zhang, Kunyang;
Fenner, Kathrin;
Wicker, Jörg

Publication type:

Article

A novel multitask learning algorithm for tasks with distinct chemical space: zebrafish toxicity prediction as an example.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00891-4

By:

Lin, Run-Hsin;
Lin, Pinpin;
Wang, Chia-Chi;
Tung, Chun-Wei

Publication type:

Article

PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00884-3

By:

Tan, Yang;
Li, Mingchen;
Zhou, Ziyi;
Tan, Pan;
Yu, Huiqun;
Fan, Guisheng;
Hong, Liang

Publication type:

Article

Implementation of a soft grading system for chemistry in a Moodle plugin: reaction handling.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00889-y

By:

Plyer, Louis;
Marcou, Gilles;
Perves, Céline;
Bonachera, Fanny;
Varnek, Alexander

Publication type:

Article

Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00886-1

By:

Zhang, Chengwei;
Zhai, Yushuang;
Gong, Ziyang;
Duan, Hongliang;
She, Yuan-Bin;
Yang, Yun-Fang;
Su, An

Publication type:

Article

Reproducible MS/MS library cleaning pipeline in matchms.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00878-1

By:

de Jonge, Niek F.;
Hecht, Helge;
Strobel, Michael;
Wang, Mingxun;
van der Hooft, Justin J. J.;
Huber, Florian

Publication type:

Article

A computational workflow for analysis of missense mutations in precision oncology.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00876-3

By:

Khan, Rayyan Tariq;
Pokorna, Petra;
Stourac, Jan;
Borko, Simeon;
Arefiev, Ihor;
Planas-Iglesias, Joan;
Dobias, Adam;
Pinto, Gaspar;
Szotkowska, Veronika;
Sterba, Jaroslav;
Slaby, Ondrej;
Damborsky, Jiri;
Mazurenko, Stanislav;
Bednar, David

Publication type:

Article

Hilbert-curve assisted structure embedding method.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00850-z

By:

Zahoránszky-Kőhalmi, Gergely;
Wan, Kanny K.;
Godfrey, Alexander G.

Publication type:

Article

CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00885-2

By:

Godinez-Macias, Karla P.;
Winzeler, Elizabeth A.

Publication type:

Article

Enhancing molecular property prediction with auxiliary learning and task-specific adaptation.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00880-7

By:

Dey, Vishal;
Ning, Xia

Publication type:

Article

Estimating the synthetic accessibility of molecules with building block and reaction-aware SAScore.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00879-0

By:

Chen, Shuan;
Jung, Yousung

Publication type:

Article

Reaction rebalancing: a novel approach to curating reaction databases.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00875-4

By:

Phan, Tieu-Long;
Weinbauer, Klaus;
Gärtner, Thomas;
Merkle, Daniel;
Andersen, Jakob L.;
Fagerberg, Rolf;
Stadler, Peter F.

Publication type:

Article

piscesCSM: prediction of anticancer synergistic drug combinations.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00859-4

By:

AlJarf, Raghad;
Rodrigues, Carlos H. M.;
Myung, Yoochan;
Pires, Douglas E. V.;
Ascher, David B.

Publication type:

Article

Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00877-2

By:

Zeng, Kaipeng;
Yang, Bo;
Zhao, Xin;
Zhang, Yu;
Nie, Fan;
Yang, Xiaokang;
Jin, Yaohui;
Xu, Yanyan

Publication type:

Article

LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00871-8

By:

Zhou, Ruifeng;
Fan, Jing;
Li, Sishu;
Zeng, Wenjie;
Chen, Yilun;
Zheng, Xiaoshan;
Chen, Hongyang;
Liao, Jun

Publication type:

Article

Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00872-7

By:

Rajan, Kohulan;
Brinkhaus, Henning Otto;
Zielesny, Achim;
Steinbeck, Christoph

Publication type:

Article

PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00866-5

By:

Thomas, Morgan;
Ahmad, Mazen;
Tresadern, Gary;
de Fabritiis, Gianni

Publication type:

Article

Application of machine reading comprehension techniques for named entity recognition in materials science.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00874-5

By:

Huang, Zihui;
He, Liqiang;
Yang, Yuhang;
Li, Andi;
Zhang, Zhiwen;
Wu, Siwei;
Wang, Yang;
He, Yan;
Liu, Xujie

Publication type:

Article

CPSign: conformal prediction for cheminformatics modeling.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00870-9

By:

Arvidsson McShane, Staffan;
Norinder, Ulf;
Alvarsson, Jonathan;
Ahlberg, Ernst;
Carlsson, Lars;
Spjuth, Ola

Publication type:

Article