Volume 14, issue 1, December 2022
89 articles in this issue
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Investigation of the structure-odor relationship using a Transformer model
Authors
- Xiaofan Zheng
- Yoichi Tomiura
- Kenshi Hayashi
- Content type: Research
- Open Access
- Published: 29 December 2022
- Article: 88
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Visualizing chemical space networks with RDKit and NetworkX
Authors
- Vincent F. Scalfani
- Vishank D. Patel
- Avery M. Fernandez
- Content type: Educational Article
- Open Access
- Published: 28 December 2022
- Article: 87
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Human-in-the-loop assisted de novo molecular design
Authors (first, second and last of 9)
- Iiris Sundin
- Alexey Voronov
- Ola Engkvist
- Content type: Research
- Open Access
- Published: 28 December 2022
- Article: 86
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An algorithm to classify homologous series within compound datasets
Authors (first, second and last of 4)
- Adelene Lai
- Jonas Schaub
- Emma L. Schymanski
- Content type: Research
- Open Access
- Published: 13 December 2022
- Article: 85
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ReMODE: a deep learning-based web server for target-specific drug design
Authors (first, second and last of 10)
- Mingyang Wang
- Jike Wang
- Tingjun Hou
- Content type: Software
- Open Access
- Published: 12 December 2022
- Article: 84
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Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder
Authors (first, second and last of 5)
- Hwanhee Kim
- Soohyun Ko
- Jaegyoon Ahn
- Content type: Research
- Open Access
- Published: 09 December 2022
- Article: 83
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Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds
Authors (first, second and last of 19)
- Jürgen Bajorath
- Ana L. Chávez-Hernández
- Marilia Valli
- Content type: Meeting Report
- Open Access
- Published: 02 December 2022
- Article: 82
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MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning
Authors (first, second and last of 6)
- Shenggeng Lin
- Weizhi Chen
- Yi Xiong
- Content type: Methodology
- Open Access
- Published: 15 November 2022
- Article: 81
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Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions
Authors (first, second and last of 4)
- Davide Boldini
- Lukas Friedrich
- Stephan A. Sieber
- Content type: Research
- Open Access
- Published: 10 November 2022
- Article: 80
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Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)
Authors (first, second and last of 4)
- Jonas Schaub
- Julian Zander
- Christoph Steinbeck
- Content type: Software
- Open Access
- Published: 10 November 2022
- Article: 79
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Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors
Authors
- Sherif Abdulkader Tawfik
- Salvy P. Russo
- Content type: Research
- Open Access
- Published: 08 November 2022
- Article: 78
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Development of machine learning classifiers to predict compound activity on prostate cancer cell lines
Authors
- Davide Bonanni
- Luca Pinzi
- Giulio Rastelli
- Content type: Research
- Open Access
- Published: 08 November 2022
- Article: 77
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Correction : Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence
Authors
- Sangjin Ahn
- Si Eun Lee
- Mi-hyun Kim
- Content type: Correction
- Open Access
- Published: 02 November 2022
- Article: 76
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VGSC-DB: an online database of voltage-gated sodium channels
Authors (first, second and last of 10)
- Gaoang Wang
- Jiahui Yu
- Tingjun Hou
- Content type: Database
- Open Access
- Published: 01 November 2022
- Article: 75
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One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data
Authors
- Luca Chiesa
- Esther Kellenberger
- Content type: Research
- Open Access
- Published: 29 October 2022
- Article: 74
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DrugTax: package for drug taxonomy identification and explainable feature extraction
Authors
- A. J. Preto
- Paulo C. Correia
- Irina S. Moreira
- Content type: Software
- Open Access
- Published: 27 October 2022
- Article: 73
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Implementation of a soft grading system for chemistry in a Moodle plugin
Authors (first, second and last of 5)
- Louis Plyer
- Gilles Marcou
- Alexandre Varnek
- Content type: Software
- Open Access
- Published: 26 October 2022
- Article: 72
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A fingerprints based molecular property prediction method using the BERT model
Authors (first, second and last of 6)
- Naifeng Wen
- Guanqun Liu
- Xu Han
- Content type: Research
- Open Access
- Published: 21 October 2022
- Article: 71
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Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules
Authors (first, second and last of 5)
- Jong Youl Choi
- Pei Zhang
- Massimiliano Lupo Pasini
- Content type: Research
- Open Access
- Published: 17 October 2022
- Article: 70
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Improving VAE based molecular representations for compound property prediction
Authors (first, second and last of 8)
- Ani Tevosyan
- Lusine Khondkaryan
- Zaven Navoyan
- Content type: Research
- Open Access
- Published: 14 October 2022
- Article: 69
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Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation
Authors (first, second and last of 4)
- Morgan Thomas
- Noel M. O’Boyle
- Chris de Graaf
- Content type: Research
- Open Access
- Published: 03 October 2022
- Article: 68
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Random-forest model for drug–target interaction prediction via Kullback–Leibler divergence
Authors
- Sangjin Ahn
- Si Eun Lee
- Mi-hyun Kim
- Content type: Research
- Open Access
- Published: 03 October 2022
- Article: 67
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TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson
Authors (first, second and last of 6)
- Jan C. Brammer
- Gerd Blanke
- Ulrich Schatzschneider
- Content type: Research
- Open Access
- Published: 28 September 2022
- Article: 66
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Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator
Authors
- Mohamed-Amine Chadi
- Hajar Mousannif
- Ahmed Aamouche
- Content type: Research
- Open Access
- Published: 27 September 2022
- Article: 65
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An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts
Authors (first, second and last of 4)
- Yasemin Yesiltepe
- Niranjan Govind
- Ryan S. Renslow
- Content type: Research article
- Open Access
- Published: 22 September 2022
- Article: 64
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What makes a reaction network “chemical”?
Authors
- Stefan Müller
- Christoph Flamm
- Peter F. Stadler
- Content type: Research article
- Open Access
- Published: 19 September 2022
- Article: 63
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Machine learning for identification of silylated derivatives from mass spectra
Authors (first, second and last of 4)
- Milka Ljoncheva
- Tomaž Stepišnik
- Sašo Džeroski
- Content type: Research
- Open Access
- Published: 15 September 2022
- Article: 62
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Review of techniques and models used in optical chemical structure recognition in images and scanned documents
Authors
- Fidan Musazade
- Narmin Jamalova
- Jamaladdin Hasanov
- Content type: Review
- Open Access
- Published: 09 September 2022
- Article: 61
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From theory to experiment: transformer-based generation enables rapid discovery of novel reactions
Authors (first, second and last of 9)
- Xinqiao Wang
- Chuansheng Yao
- Hongliang Duan
- Content type: Research article
- Open Access
- Published: 02 September 2022
- Article: 60
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Robustness under parameter and problem domain alterations of Bayesian optimization methods for chemical reactions
Authors (first, second and last of 5)
- Rubaiyat Mohammad Khondaker
- Stephen Gow
- Mahesan Niranjan
- Content type: Research
- Open Access
- Published: 01 September 2022
- Article: 59
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FPocketWeb: protein pocket hunting in a web browser
Authors
- Yuri Kochnev
- Jacob D. Durrant
- Content type: Software
- Open Access
- Published: 26 August 2022
- Article: 58
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European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials
Authors (first, second and last of 14)
- Jeaphianne van Rijn
- Antreas Afantitis
- Egon Willighagen
- Content type: Research article
- Open Access
- Published: 24 August 2022
- Article: 57
This is part of 1 collection: -
Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses
Authors (first, second and last of 6)
- Yang Yu
- Zhe Wang
- Huiyong Sun
- Content type: Research
- Open Access
- Published: 20 August 2022
- Article: 56
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Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach
Authors (first, second and last of 5)
- O. A. Tarasova
- A. V. Rudik
- V. V. Poroikov
- Content type: Research
- Open Access
- Published: 13 August 2022
- Article: 55
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Using Jupyter Notebooks for re-training machine learning models
Authors
- Aljoša Smajić
- Melanie Grandits
- Gerhard F. Ecker
- Content type: Educational
- Open Access
- Published: 13 August 2022
- Article: 54
This is part of 1 collection: -
Correction to: Designing optimized drug candidates with Generative Adversarial Network
Authors (first, second and last of 10)
- Maryam Abbasi
- Beatriz P. Santos
- Joel P. Arrais
- Content type: Correction
- Open Access
- Published: 11 August 2022
- Article: 53
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Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation
Authors (first, second and last of 9)
- Yue Kong
- Xiaoman Zhao
- Aixia Yan
- Content type: Research article
- Open Access
- Published: 04 August 2022
- Article: 52
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Paths to Cheminformatics: Q&A with Norberto Sánchez-Cruz and Emma Schymanski
Authors
- Norberto Sánchez-Cruz
- Emma L. Schymanski
- Content type: Question And Answer
- Open Access
- Published: 02 August 2022
- Article: 51
This is part of 1 collection: -
Confidence bands and hypothesis tests for hit enrichment curves
Authors
- Jeremy R Ash
- Jacqueline M Hughes-Oliver
- Content type: Methodology
- Open Access
- Published: 28 July 2022
- Article: 50
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SimVec: predicting polypharmacy side effects for new drugs
Authors (first, second and last of 5)
- Nina Lukashina
- Elena Kartysheva
- Aleksei Shpilman
- Content type: Methodology
- Open Access
- Published: 26 July 2022
- Article: 49
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Machine intelligence-driven framework for optimized hit selection in virtual screening
Authors
- Neeraj Kumar
- Vishal Acharya
- Content type: Methodology
- Open Access
- Published: 22 July 2022
- Article: 48
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Predicting protein network topology clusters from chemical structure using deep learning
Authors (first, second and last of 6)
- Akshai P. Sreenivasan
- Philip J Harrison
- Ola Spjuth
- Content type: Research article
- Open Access
- Published: 15 July 2022
- Article: 47
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In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network
Authors (first, second and last of 7)
- Mengting Huang
- Chaofeng Lou
- Guixia Liu
- Content type: Research
- Open Access
- Published: 08 July 2022
- Article: 46
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BitterMatch: recommendation systems for matching molecules with bitter taste receptors
Authors (first, second and last of 6)
- Eitan Margulis
- Yuli Slavutsky
- Masha Y. Niv
- Content type: Research
- Open Access
- Published: 07 July 2022
- Article: 45
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Blood–brain barrier penetration prediction enhanced by uncertainty estimation
Authors (first, second and last of 12)
- Xiaochu Tong
- Dingyan Wang
- Xutong Li
- Content type: Research article
- Open Access
- Published: 07 July 2022
- Article: 44
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LigninGraphs: lignin structure determination with multiscale graph modeling
Authors (first, second and last of 5)
- Yifan Wang
- Jake Kalscheur
- Dionisios G. Vlachos
- Content type: Software
- Open Access
- Published: 06 July 2022
- Article: 43
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Correction to: Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs
Authors
- Kedan He
- Content type: Correction
- Open Access
- Published: 03 July 2022
- Article: 42
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SwinOCSR: end-to-end optical chemical structure recognition using a Swin Transformer
Authors (first, second and last of 5)
- Zhanpeng Xu
- Jianhua Li
- Honglin Li
- Content type: Research
- Open Access
- Published: 01 July 2022
- Article: 41
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Designing optimized drug candidates with Generative Adversarial Network
Authors (first, second and last of 10)
- Maryam Abbasi
- Beatriz P. Santos
- Joel P. Arrais
- Content type: Research
- Open Access
- Published: 26 June 2022
- Article: 40