Works matching IS 17582946 AND DT 2023

Results: 134

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00794-w

By:

Baillif, Benoit;
Cole, Jason;
Giangreco, Ilenia;
McCabe, Patrick;
Bender, Andreas

Publication type:

Article

A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00780-2

By:

Vaitkus, Antanas;
Merkys, Andrius;
Sander, Thomas;
Quirós, Miguel;
Thiessen, Paul A.;
Bolton, Evan E.;
Gražulis, Saulius

Publication type:

Article

Ilm-NMR-P31: an open-access <sup>31</sup>P nuclear magnetic resonance database and data-driven prediction of <sup>31</sup>P NMR shifts.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00792-y

By:

Hack, Jasmin;
Jordan, Moritz;
Schmitt, Alina;
Raru, Melissa;
Zorn, Hannes Sönke;
Seyfarth, Alex;
Eulenberger, Isabel;
Geitner, Robert

Publication type:

Article

Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00790-0

By:

Rasmussen, Maria H.;
Duan, Chenru;
Kulik, Heather J.;
Jensen, Jan H.

Publication type:

Article

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

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00791-z

By:

Shimizu, Yugo;
Ohta, Masateru;
Ishida, Shoichi;
Terayama, Kei;
Osawa, Masanori;
Honma, Teruki;
Ikeda, Kazuyoshi

Publication type:

Article

SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00787-9

By:

Landrum, Gregory A.;
Beckers, Maximilian;
Lanini, Jessica;
Schneider, Nadine;
Stiefl, Nikolaus;
Riniker, Sereina

Publication type:

Article

HybridGCN for protein solubility prediction with adaptive weighting of multiple features.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00788-8

By:

Chen, Long;
Wu, Rining;
Zhou, Feixiang;
Zhang, Huifeng;
Liu, Jian K.

Publication type:

Article

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00786-w

By:

Kunnakkattu, Ibrahim Roshan;
Choudhary, Preeti;
Pravda, Lukas;
Nadzirin, Nurul;
Smart, Oliver S.;
Yuan, Qi;
Anyango, Stephen;
Nair, Sreenath;
Varadi, Mihaly;
Velankar, Sameer

Publication type:

Article

Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00782-0

By:

Lehembre, Etienne;
Giovannini, Johanna;
Geslin, Damien;
Lepailleur, Alban;
Lamotte, Jean-Luc;
Auber, David;
Ouali, Abdelkader;
Cremilleux, Bruno;
Zimmermann, Albrecht;
Cuissart, Bertrand;
Bureau, Ronan

Publication type:

Article

EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00779-9

By:

Xu, Hong-Quan;
Xiao, Huan;
Bu, Jin-Hui;
Hong, Yan-Feng;
Liu, Yu-Hong;
Tao, Zi-Yue;
Ding, Shu-Fan;
Xia, Yi-Tong;
Wu, E;
Yan, Zhen;
Zhang, Wei;
Chen, Gong-Xing;
Zhu, Feng;
Tao, Lin

Publication type:

Article

NMR shift prediction from small data quantities.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00785-x

By:

Rull, Herman;
Fischer, Markus;
Kuhn, Stefan

Publication type:

Article

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00784-y

By:

Probst, Daniel

Publication type:

Article

On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00781-1

By:

Handa, Koichi;
Thomas, Morgan C.;
Kageyama, Michiharu;
Iijima, Takeshi;
Bender, Andreas

Publication type:

Article

YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00783-z

By:

Zhou, Chong;
Liu, Wei;
Song, Xiyue;
Yang, Mengling;
Peng, Xiaowang

Publication type:

Article

BBB-PEP-prediction: improved computational model for identification of blood–brain barrier peptides using blending position relative composition specific features and ensemble modeling.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00773-1

By:

Naseem, Ansar;
Alturise, Fahad;
Alkhalifah, Tamim;
Khan, Yaser Daanial

Publication type:

Article

Art driven by visual representations of chemical space.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00770-4

By:

Gaytán-Hernández, Daniela;
Chávez-Hernández, Ana L.;
López-López, Edgar;
Miranda-Salas, Jazmín;
Saldívar-González, Fernanda I.;
Medina-Franco, José L.

Publication type:

Article

rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00756-2

By:

Baquer, Gerard;
Sementé, Lluc;
Ràfols, Pere;
Martín-Saiz, Lucía;
Bookmeyer, Christoph;
Fernández, José A.;
Correig, Xavier;
García-Altares, María

Publication type:

Article

Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00755-3

By:

Hadfield, Thomas E.;
Scantlebury, Jack;
Deane, Charlotte M.

Publication type:

Article

LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00754-4

By:

Wang, Yitian;
Xiong, Jiacheng;
Xiao, Fu;
Zhang, Wei;
Cheng, Kaiyang;
Rao, Jingxin;
Niu, Buying;
Tong, Xiaochu;
Qu, Ning;
Zhang, Runze;
Wang, Dingyan;
Chen, Kaixian;
Li, Xutong;
Zheng, Mingyue

Publication type:

Article

Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00752-6

By:

Tayyebi, Arash;
Alshami, Ali S;
Rabiei, Zeinab;
Yu, Xue;
Ismail, Nadhem;
Talukder, Musabbir Jahan;
Power, Jason

Publication type:

Article

Extended study on atomic featurization in graph neural networks for molecular property prediction.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00751-7

By:

Wojtuch, Agnieszka;
Danel, Tomasz;
Podlewska, Sabina;
Maziarka, Łukasz

Publication type:

Article

Paths to cheminformatics: Q&A with Nathaniel Charest.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00750-8

By:

Charest, Nathaniel

Publication type:

Article

DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00738-4

By:

Kim, Hyun Woo;
Zhang, Chen;
Reher, Raphael;
Wang, Mingxun;
Alexander, Kelsey L.;
Nothias, Louis-Félix;
Han, Yoo Kyong;
Shin, Hyeji;
Lee, Ki Yong;
Lee, Kyu Hyeong;
Kim, Myeong Ji;
Dorrestein, Pieter C.;
Gerwick, William H.;
Cottrell, Garrison W.

Publication type:

Article

HD_BPMDS: a curated binary pattern multitarget dataset of Huntington's disease–targeting agents.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00775-z

By:

Stefan, Sven Marcel;
Pahnke, Jens;
Namasivayam, Vigneshwaran

Publication type:

Article

Correction: MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal–organic frameworks utilizing graph convolutional networks.

Published in:

2023

By:

Jalali, Mehrdad;
Wonanke, A. D. Dinga;
Wöll, Christof

Publication type:

Correction Notice

MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal–organic frameworks utilizing graph convolutional networks.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00764-2

By:

Jalali, Mehrdad;
Wonanke, A. D. Dinga;
Wöll, Christof

Publication type:

Article

Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00778-w

By:

Domingo-Fernández, Daniel;
Gadiya, Yojana;
Mubeen, Sarah;
Healey, David;
Norman, Bryan H.;
Colluru, Viswa

Publication type:

Article

Continuous symmetry and chirality measures: approximate algorithms for large molecular structures.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00777-x

By:

Alon, Gil;
Ben-Haim, Yuval;
Tuvi-Arad, Inbal

Publication type:

Article

Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00753-5

By:

Yin, Tianzhixi;
Panapitiya, Gihan;
Coda, Elizabeth D.;
Saldanha, Emily G.

Publication type:

Article

Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00776-y

By:

Li, Sean;
Bohman, Björn;
Flematti, Gavin R.;
Jayatilaka, Dylan

Publication type:

Article

DeepSA: a deep-learning driven predictor of compound synthesis accessibility.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00771-3

By:

Wang, Shihang;
Wang, Lin;
Li, Fenglei;
Bai, Fang

Publication type:

Article

EasyDock: customizable and scalable docking tool.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00772-2

By:

Minibaeva, Guzel;
Ivanova, Aleksandra;
Polishchuk, Pavel

Publication type:

Article

DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00769-x

By:

Fralish, Zachary;
Chen, Ashley;
Skaluba, Paul;
Reker, Daniel

Publication type:

Article

Art driven by visual representations of chemical space.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00770-4

By:

Gaytán-Hernández, Daniela;
Chávez-Hernández, Ana L.;
López-López, Edgar;
Miranda-Salas, Jazmín;
Saldívar-González, Fernanda I.;
Medina-Franco, José L.

Publication type:

Article

Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00752-6

By:

Tayyebi, Arash;
Alshami, Ali S;
Rabiei, Zeinab;
Yu, Xue;
Ismail, Nadhem;
Talukder, Musabbir Jahan;
Power, Jason

Publication type:

Article

Cheminformatics Microservice: unifying access to open cheminformatics toolkits.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00762-4

By:

Chandrasekhar, Venkata;
Sharma, Nisha;
Schaub, Jonas;
Steinbeck, Christoph;
Rajan, Kohulan

Publication type:

Article

Pmf-cpi: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00767-z

By:

Song, Nan;
Dong, Ruihan;
Pu, Yuqian;
Wang, Ercheng;
Xu, Junhai;
Guo, Fei

Publication type:

Article

Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00768-y

By:

Gil-Pichardo, Alberto;
Sánchez-Ruiz, Andrés;
Colmenarejo, Gonzalo

Publication type:

Article

Bloom filters for molecules.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00765-1

By:

Medina, Jorge;
White, Andrew D.

Publication type:

Article

MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal–organic frameworks utilizing graph convolutional networks.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00764-2

By:

Jalali, Mehrdad;
Wonanke, A. D. Dinga;
Wöll, Christof

Publication type:

Article

Paths to cheminformatics: Q&A with Nathaniel Charest.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00750-8

By:

Charest, Nathaniel

Publication type:

Article

Paths to cheminformatics: Q&A with Ann M. Richard.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00749-1

By:

Richard, Ann M.

Publication type:

Article

ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00766-0

By:

Hu, Chao;
Li, Song;
Yang, Chenxing;
Chen, Jun;
Xiong, Yi;
Fan, Guisheng;
Liu, Hao;
Hong, Liang

Publication type:

Article

Reliable and accurate prediction of basic pKa values in nitrogen compounds: the pKa shift in supramolecular systems as a case study.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00763-3

By:

Alcázar, Jackson J.;
Misad Saide, Alessandra C.;
Campodónico, Paola R.

Publication type:

Article

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

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00761-5

By:

Kerstjens, Alan;
De Winter, Hans

Publication type:

Article

Extended study on atomic featurization in graph neural networks for molecular property prediction.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00751-7

By:

Wojtuch, Agnieszka;
Danel, Tomasz;
Podlewska, Sabina;
Maziarka, Łukasz

Publication type:

Article

Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00760-6

By:

Durai, Prasannavenkatesh;
Lee, Sue Jung;
Lee, Jae Wook;
Pan, Cheol-Ho;
Park, Keunwan

Publication type:

Article

Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00741-9

By:

Hu, Ximin;
Mar, Derek;
Suzuki, Nozomi;
Zhang, Bowei;
Peter, Katherine T.;
Beck, David A. C.;
Kolodziej, Edward P.

Publication type:

Article

School of cheminformatics in Latin America.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00758-0

By:

Gonzalez-Ponce, Karla;
Horta Andrade, Carolina;
Hunter, Fiona;
Kirchmair, Johannes;
Martinez-Mayorga, Karina;
Medina-Franco, José L.;
Rarey, Matthias;
Tropsha, Alexander;
Varnek, Alexandre;
Zdrazil, Barbara

Publication type:

Article

Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00755-3

By:

Hadfield, Thomas E.;
Scantlebury, Jack;
Deane, Charlotte M.

Publication type:

Article