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

Results: 135

DeepTGIN: a novel hybrid multimodal approach using transformers and graph isomorphism networks for protein-ligand binding affinity prediction.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00938-6

By:

Wang, Guishen;
Zhang, Hangchen;
Shao, Mengting;
Feng, Yuncong;
Cao, Chen;
Hu, Xiaowen

Publication type:

Article

STOUT V2.0: SMILES to IUPAC name conversion using transformer models.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00941-x

By:

Rajan, Kohulan;
Zielesny, Achim;
Steinbeck, Christoph

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

Comprehensive benchmarking of computational tools for predicting toxicokinetic and physicochemical properties of chemicals.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00931-z

By:

Gadaleta, Domenico;
Serrano-Candelas, Eva;
Ortega-Vallbona, Rita;
Colombo, Erika;
Garcia de Lomana, Marina;
Biava, Giada;
Aparicio-Sánchez, Pablo;
Roncaglioni, Alessandra;
Gozalbes, Rafael;
Benfenati, Emilio

Publication type:

Article

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

Published in:

2024

By:

Ivanova, Aleksandra;
Mokshyna, Olena;
Polishchuk, Pavel

Publication type:

Correction Notice

AttenhERG: a reliable and interpretable graph neural network framework for predicting hERG channel blockers.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00940-y

By:

Yang, Tianbiao;
Ding, Xiaoyu;
McMichael, Elizabeth;
Pun, Frank W.;
Aliper, Alex;
Ren, Feng;
Zhavoronkov, Alex;
Ding, Xiao

Publication type:

Article

Interface-aware molecular generative framework for protein–protein interaction modulators.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00930-0

By:

Wang, Jianmin;
Mao, Jiashun;
Li, Chunyan;
Xiang, Hongxin;
Wang, Xun;
Wang, Shuang;
Wang, Zixu;
Chen, Yangyang;
Li, Yuquan;
No, Kyoung Tai;
Song, Tao;
Zeng, Xiangxiang

Publication type:

Article

MolNexTR: a generalized deep learning model for molecular image recognition.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00926-w

By:

Chen, Yufan;
Leung, Ching Ting;
Huang, Yong;
Sun, Jianwei;
Chen, Hao;
Gao, Hanyu

Publication type:

Article

FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00935-9

By:

Herrera-Rocha, Fabio;
Fernández-Niño, Miguel;
Duitama, Jorge;
Cala, Mónica P.;
Chica, María José;
Wessjohann, Ludger A.;
Davari, Mehdi D.;
Barrios, Andrés Fernando González

Publication type:

Article

Be aware of overfitting by hyperparameter optimization!

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00934-w

By:

Tetko, Igor V.;
van Deursen, Ruud;
Godin, Guillaume

Publication type:

Article

Human-in-the-loop active learning for goal-oriented molecule generation.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00924-y

By:

Nahal, Yasmine;
Menke, Janosch;
Martinelli, Julien;
Heinonen, Markus;
Kabeshov, Mikhail;
Janet, Jon Paul;
Nittinger, Eva;
Engkvist, Ola;
Kaski, Samuel

Publication type:

Article

Deepmol: an automated machine and deep learning framework for computational chemistry.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00937-7

By:

Correia, João;
Capela, João;
Rocha, Miguel

Publication type:

Article

CSearch: chemical space search via virtual synthesis and global optimization.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00936-8

By:

Kim, Hakjean;
Ryu, Seongok;
Jung, Nuri;
Yang, Jinsol;
Seok, Chaok

Publication type:

Article

Sort & Slice: a simple and superior alternative to hash-based folding for extended-connectivity fingerprints.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00932-y

By:

Dablander, Markus;
Hanser, Thierry;
Lambiotte, Renaud;
Morris, Garrett M.

Publication type:

Article

Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00933-x

By:

Cao, Piao-Yang;
He, Yang;
Cui, Ming-Yang;
Zhang, Xiao-Min;
Zhang, Qingye;
Zhang, Hong-Yu

Publication type:

Article

cidalsDB: an AI-empowered platform for anti-pathogen therapeutics research.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00929-7

By:

Harigua-Souiai, Emna;
Masmoudi, Ons;
Makni, Samer;
Oualha, Rafeh;
Abdelkrim, Yosser Z.;
Hamdi, Sara;
Souiai, Oussama;
Guizani, Ikram

Publication type:

Article

Suitability of large language models for extraction of high-quality chemical reaction dataset from patent literature.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00928-8

By:

Vangala, Sarveswara Rao;
Krishnan, Sowmya Ramaswamy;
Bung, Navneet;
Nandagopal, Dhandapani;
Ramasamy, Gomathi;
Kumar, Satyam;
Sankaran, Sridharan;
Srinivasan, Rajgopal;
Roy, Arijit

Publication type:

Article

GT-NMR: a novel graph transformer-based approach for accurate prediction of NMR chemical shifts.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00927-9

By:

Chen, Haochen;
Liang, Tao;
Tan, Kai;
Wu, Anan;
Lu, Xin

Publication type:

Article

Molecular identification via molecular fingerprint extraction from atomic force microscopy images.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00921-1

By:

González Lastre, Manuel;
Pou, Pablo;
Wiche, Miguel;
Ebeling, Daniel;
Schirmeisen, Andre;
Pérez, Rubén

Publication type:

Article

A systematic review of deep learning chemical language models in recent era.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00916-y

By:

Flores-Hernandez, Hector;
Martinez-Ledesma, Emmanuel

Publication type:

Article

Accelerated hit identification with target evaluation, deep learning and automated labs: prospective validation in IRAK1.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00914-0

By:

Kamuntavičius, Gintautas;
Prat, Alvaro;
Paquet, Tanya;
Bastas, Orestis;
Aty, Hisham Abdel;
Sun, Qing;
Andersen, Carsten B.;
Harman, John;
Siladi, Marc E.;
Rines, Daniel R.;
Flatters, Sarah J. L.;
Tal, Roy;
Norvaišas, Povilas

Publication type:

Article

QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00908-y

By:

van den Maagdenberg, Helle W.;
Šícho, Martin;
Araripe, David Alencar;
Luukkonen, Sohvi;
Schoenmaker, Linde;
Jespers, Michiel;
Béquignon, Olivier J. M.;
González, Marina Gorostiola;
van den Broek, Remco L.;
Bernatavicius, Andrius;
van Hasselt, J. G. Coen;
van der Graaf, Piet. H.;
van Westen, Gerard J. P.

Publication type:

Article

Comparative evaluation of methods for the prediction of protein–ligand binding sites.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00923-z

By:

Utgés, Javier S.;
Barton, Geoffrey J.

Publication type:

Article

Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00920-2

By:

Wang, Jue;
Liu, Yufan;
Tian, Boxue

Publication type:

Article

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