Volume 14, issue 1, December 2022
89 articles in this issue
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Commentary: the first twelve years of the Journal of Cheminformatics
Authors
- Peter Willett
- Content type: Comment
- Open Access
- Published: 13 June 2022
- Article: 38
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KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study
Authors (first, second and last of 5)
- Barbara Füzi
- Rahuman S. Malik-Sheriff
- Gerhard F. Ecker
- Content type: Research article
- Open Access
- Published: 13 June 2022
- Article: 37
This is part of 1 collection: -
DECIMER—hand-drawn molecule images dataset
Authors (first, second and last of 4)
- Henning Otto Brinkhaus
- Achim Zielesny
- Kohulan Rajan
- Content type: Data Note
- Open Access
- Published: 09 June 2022
- Article: 36
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Pharmacological affinity fingerprints derived from bioactivity data for the identification of designer drugs
Authors
- Kedan He
- Content type: Research article
- Open Access
- Published: 07 June 2022
- Article: 35
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PIKAChU: a Python-based informatics kit for analysing chemical units
Authors
- Barbara R. Terlouw
- Sophie P. J. M. Vromans
- Marnix H. Medema
- Content type: Software
- Open Access
- Published: 07 June 2022
- Article: 34
This is part of 1 collection: -
Probabilistic metabolite annotation using retention time prediction and meta-learned projections
Authors (first, second and last of 4)
- Constantino A. GarcÃa
- Alberto Gil-de-la-Fuente
- Abraham Otero
- Content type: Research article
- Open Access
- Published: 07 June 2022
- Article: 33
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Analysis of the benefits of imputation models over traditional QSAR models for toxicity prediction
Authors (first, second and last of 5)
- Moritz Walter
- Luke N. Allen
- Valerie J. Gillet
- Content type: Research
- Open Access
- Published: 07 June 2022
- Article: 32
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RanDepict: Random chemical structure depiction generator
Authors (first, second and last of 4)
- Henning Otto Brinkhaus
- Kohulan Rajan
- Christoph Steinbeck
- Content type: Software
- Open Access
- Published: 06 June 2022
- Article: 31
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InflamNat: web-based database and predictor of anti-inflammatory natural products
Authors (first, second and last of 7)
- Ruihan Zhang
- Shoupeng Ren
- Weilie Xiao
- Content type: Research article
- Open Access
- Published: 04 June 2022
- Article: 30
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Chemical reaction network knowledge graphs: the OntoRXN ontology
Authors
- Diego Garay-Ruiz
- Carles Bo
- Content type: Research
- Open Access
- Published: 30 May 2022
- Article: 29
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canSAR chemistry registration and standardization pipeline
Authors (first, second and last of 6)
- Daniela Dolciami
- Eloy Villasclaras-Fernandez
- Albert A. Antolin
- Content type: Methodology
- Open Access
- Published: 28 May 2022
- Article: 28
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Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules
Authors (first, second and last of 4)
- Doha Naga
- Wolfgang Muster
- Gerhard F. Ecker
- Content type: Research article
- Open Access
- Published: 07 May 2022
- Article: 27
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Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond
Authors (first, second and last of 5)
- Huanyu Tao
- Qilong Wu
- Sheng-You Huang
- Content type: Methodology
- Open Access
- Published: 03 May 2022
- Article: 26
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Diversifying cheminformatics
Authors
- Barbara Zdrazil
- Rajarshi Guha
- Content type: Editorial
- Open Access
- Published: 25 April 2022
- Article: 25
This is part of 1 collection: -
Surge: a fast open-source chemical graph generator
Authors
- Brendan D. McKay
- Mehmet Aziz Yirik
- Christoph Steinbeck
- Content type: Software
- Open Access
- Published: 23 April 2022
- Article: 24
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Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes
Authors (first, second and last of 9)
- Ning-Ning Wang
- Xiang-Gui Wang
- Dong-Sheng Cao
- Content type: Research article
- Open Access
- Published: 15 April 2022
- Article: 23
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
Authors (first, second and last of 6)
- Simon Bray
- Tim Dudgeon
- Frank von Delft
- Content type: Research article
- Open Access
- Published: 12 April 2022
- Article: 22
This is part of 1 collection: -
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations
Authors (first, second and last of 8)
- Christina Humer
- Henry Heberle
- Marc Streit
- Content type: Software
- Open Access
- Published: 04 April 2022
- Article: 21
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Explaining and avoiding failure modes in goal-directed generation of small molecules
Authors
- Maxime Langevin
- Rodolphe Vuilleumier
- Marc Bianciotto
- Content type: Research article
- Open Access
- Published: 01 April 2022
- Article: 20
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Systemic evolutionary chemical space exploration for drug discovery
Authors (first, second and last of 10)
- Chong Lu
- Shien Liu
- Yikai Wang
- Content type: Software
- Open Access
- Published: 01 April 2022
- Article: 19
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Transformer-based molecular optimization beyond matched molecular pairs
Authors (first, second and last of 7)
- Jiazhen He
- Eva Nittinger
- Ola Engkvist
- Content type: Research article
- Open Access
- Published: 28 March 2022
- Article: 18
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Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening
Authors (first, second and last of 4)
- Melissa F. Adasme
- Sarah Naomi Bolz
- Michael Schroeder
- Content type: Research article
- Open Access
- Published: 15 March 2022
- Article: 17
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A multitask GNN-based interpretable model for discovery of selective JAK inhibitors
Authors (first, second and last of 8)
- Yimeng Wang
- Yaxin Gu
- Guixia Liu
- Content type: Research article
- Open Access
- Published: 15 March 2022
- Article: 16
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Improving the performance of models for one-step retrosynthesis through re-ranking
Authors
- Min Htoo Lin
- Zhengkai Tu
- Connor W. Coley
- Content type: Research article
- Open Access
- Published: 15 March 2022
- Article: 15
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ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding
Authors (first, second and last of 5)
- Junjie Wang
- NaiFeng Wen
- Liang Cheng
- Content type: Research article
- Open Access
- Published: 15 March 2022
- Article: 14
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Correction to: TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids
Authors
- David Ferro‑Costas
- Irea Mosquera‑Lois
- Antonio Fernandez‑Ramos
- Content type: Correction
- Open Access
- Published: 14 March 2022
- Article: 13
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Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles
Authors (first, second and last of 9)
- Chengyou Liu
- Andrew M. Hogan
- Pingzhao Hu
- Content type: Research article
- Open Access
- Published: 12 March 2022
- Article: 12
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Application of deep metric learning to molecular graph similarity
Authors
- Damien E. Coupry
- Peter Pogány
- Content type: Research article
- Open Access
- Published: 12 March 2022
- Article: 11
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MolData, a molecular benchmark for disease and target based machine learning
Authors (first, second and last of 4)
- Arash Keshavarzi Arshadi
- Milad Salem
- Jiann Shiun Yuan
- Content type: Research article
- Open Access
- Published: 07 March 2022
- Article: 10
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DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions
Authors
- Eunyoung Kim
- Hojung Nam
- Content type: Research article
- Open Access
- Published: 04 March 2022
- Article: 9
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PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow
Authors (first, second and last of 4)
- Ammar Ammar
- Rachel Cavill
- Egon Willighagen
- Content type: Database
- Open Access
- Published: 28 February 2022
- Article: 8
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GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations
Authors
- Michael Freitas Gustavo
- Toon Verstraelen
- Content type: Software
- Open Access
- Published: 16 February 2022
- Article: 7
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Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features
Authors
- Miao Yu
- Georgia Dolios
- Lauren Petrick
- Content type: Research article
- Open Access
- Published: 16 February 2022
- Article: 6
This is part of 1 collection: -
Sequence-based prediction of protein binding regions and drug–target interactions
Authors
- Ingoo Lee
- Hojung Nam
- Content type: Research article
- Open Access
- Published: 08 February 2022
- Article: 5
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Machine learning approaches to optimize small-molecule inhibitors for RNA targeting
Authors (first, second and last of 7)
- Hadar Grimberg
- Vinay S. Tiwari
- Barak Akabayov
- Content type: Research article
- Open Access
- Published: 02 February 2022
- Article: 4
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LEADD: Lamarckian evolutionary algorithm for de novo drug design
Authors
- Alan Kerstjens
- Hans De Winter
- Content type: Research article
- Open Access
- Published: 15 January 2022
- Article: 3
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Uncertainty-aware prediction of chemical reaction yields with graph neural networks
Authors (first, second and last of 4)
- Youngchun Kwon
- Dongseon Lee
- Seokho Kang
- Content type: Research article
- Open Access
- Published: 10 January 2022
- Article: 2
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HobPre: accurate prediction of human oral bioavailability for small molecules
Authors (first, second and last of 7)
- Min Wei
- Xudong Zhang
- John Z. H. Zhang
- Content type: Research article
- Open Access
- Published: 06 January 2022
- Article: 1