Volume 11, issue 1, December 2019
80 articles in this issue
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Learning important features from multi-view data to predict drug side effects
Authors (first, second and last of 7)
- Xujun Liang
- Pengfei Zhang
- Zhuchu Chen
- Content type: Research article
- Open Access
- Published: 16 December 2019
- Article: 79
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IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting
Authors
- Pei-Hua Wang
- Yufeng Jane Tseng
- Content type: Software
- Open Access
- Published: 11 December 2019
- Article: 78
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ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
Authors (first, second and last of 5)
- An Nguyen
- Yu-Chieh Huang
- Stefan Bräse
- Content type: Software
- Open Access
- Published: 11 December 2019
- Article: 77
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The chemfp project
Authors
- Andrew Dalke
- Content type: Methodology
- Open Access
- Published: 05 December 2019
- Article: 76
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HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Authors
- Julien Wist
- Content type: Research article
- Open Access
- Published: 05 December 2019
- Article: 75
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A de novo molecular generation method using latent vector based generative adversarial network
Authors (first, second and last of 7)
- Oleksii Prykhodko
- Simon Viet Johansson
- Hongming Chen
- Content type: Research article
- Open Access
- Published: 03 December 2019
- Article: 74
This is part of 1 collection: -
ACID: a free tool for drug repurposing using consensus inverse docking strategy
Authors (first, second and last of 7)
- Fan Wang
- Feng-Xu Wu
- Guang-Fu Yang
- Content type: Research article
- Open Access
- Published: 27 November 2019
- Article: 73
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A comprehensive analysis of the history of DFT based on the bibliometric method RPYS
Authors
- Robin Haunschild
- Andreas Barth
- Bernie French
- Content type: Research article
- Open Access
- Published: 21 November 2019
- Article: 72
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Randomized SMILES strings improve the quality of molecular generative models
Authors (first, second and last of 8)
- Josep Arús-Pous
- Simon Viet Johansson
- Ola Engkvist
- Content type: Research article
- Open Access
- Published: 21 November 2019
- Article: 71
This is part of 1 collection: -
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation
Authors (first, second and last of 6)
- Youngchun Kwon
- Jiho Yoo
- Seokho Kang
- Content type: Research article
- Open Access
- Published: 21 November 2019
- Article: 70
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Dataset’s chemical diversity limits the generalizability of machine learning predictions
Authors (first, second and last of 5)
- Marta Glavatskikh
- Jules Leguy
- Benoit Da Mota
- Content type: Research article
- Open Access
- Published: 12 November 2019
- Article: 69
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Multi-task learning with a natural metric for quantitative structure activity relationship learning
Authors (first, second and last of 9)
- Noureddin Sadawi
- Ivan Olier
- Ross D. King
- Content type: Research article
- Open Access
- Published: 12 November 2019
- Article: 68
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Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening
Authors (first, second and last of 7)
- Anna Lovrics
- Veronika F. S. Pape
- Gergely Szakács
- Content type: Research article
- Open Access
- Published: 09 November 2019
- Article: 67
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A multiple classifier system identifies novel cannabinoid CB2 receptor ligands
Authors (first, second and last of 9)
- David Ruano-Ordás
- Lindsey Burggraaff
- Gerard J. P. van Westen
- Content type: Research article
- Open Access
- Published: 07 November 2019
- Article: 66
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Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery
Authors
- Damjan Krstajic
- Content type: Letter to the Editor
- Open Access
- Published: 06 November 2019
- Article: 65
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Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”
Authors (first, second and last of 6)
- Nicolas Bosc
- Francis Atkinson
- Andrew R. Leach
- Content type: Letter to the Editor
- Open Access
- Published: 06 November 2019
- Article: 64
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A visual approach for analysis and inference of molecular activity spaces
Authors
- Samina Kausar
- Andre O. Falcao
- Content type: Research article
- Open Access
- Published: 22 October 2019
- Article: 63
This is part of 1 collection: -
A path to next-generation reproducibility in cheminformatics
Authors
- Robert D. Clark
- Content type: Commentary
- Open Access
- Published: 14 October 2019
- Article: 62
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A general approach for retrosynthetic molecular core analysis
Authors (first, second and last of 4)
- J. Jesús Naveja
- B. Angélica Pilón-Jiménez
- José L. Medina-Franco
- Content type: Methodology
- Open Access
- Published: 24 September 2019
- Article: 61
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Open-source QSAR models for pKa prediction using multiple machine learning approaches
Authors (first, second and last of 10)
- Kamel Mansouri
- Neal F. Cariello
- Antony J. Williams
- Content type: Research article
- Open Access
- Published: 18 September 2019
- Article: 60
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Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies
Authors
- Christoph A. Bauer
- Gisbert Schneider
- Andreas H. Göller
- Content type: Research article
- Open Access
- Published: 11 September 2019
- Article: 59
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SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data
Authors (first, second and last of 9)
- Domenico Gadaleta
- Kristijan Vuković
- Alessandra Roncaglioni
- Content type: Research article
- Open Access
- Published: 30 August 2019
- Article: 58
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Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model
Authors
- Simon Müller
- Content type: Research article
- Open Access
- Published: 20 August 2019
- Article: 57
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PUG-View: programmatic access to chemical annotations integrated in PubChem
Authors (first, second and last of 6)
- Sunghwan Kim
- Paul A. Thiessen
- Evan E. Bolton
- Content type: Database
- Open Access
- Published: 09 August 2019
- Article: 56
This is part of 1 collection: -
NaPLeS: a natural products likeness scorer—web application and database
Authors
- Maria Sorokina
- Christoph Steinbeck
- Content type: Software
- Open Access
- Published: 09 August 2019
- Article: 55
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Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability
Authors (first, second and last of 5)
- Oliver Laufkötter
- Noé Sturm
- Ola Engkvist
- Content type: Research article
- Open Access
- Published: 08 August 2019
- Article: 54
This is part of 1 collection: -
Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s
Authors (first, second and last of 4)
- Joel Wahl
- Joel Freyss
- Thomas Sander
- Content type: Research article
- Open Access
- Published: 07 August 2019
- Article: 53
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DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state
Authors (first, second and last of 9)
- Pin Chen
- Yaobin Ke
- Yuedong Yang
- Content type: Research article
- Open Access
- Published: 07 August 2019
- Article: 52
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Correction to: A new topological descriptor for water network structure
Authors
- Lee Steinberg
- John Russo
- Jeremy Frey
- Content type: Correction
- Open Access
- Published: 07 August 2019
- Article: 51
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Rapid prediction of NMR spectral properties with quantified uncertainty
Authors
- Eric Jonas
- Stefan Kuhn
- Content type: Research article
- Open Access
- Published: 06 August 2019
- Article: 50
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Fast, efficient fragment-based coordinate generation for Open Babel
Authors
- Naruki Yoshikawa
- Geoffrey R. Hutchison
- Content type: Software
- Open Access
- Published: 01 August 2019
- Article: 49
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A new topological descriptor for water network structure
Authors
- Lee Steinberg
- John Russo
- Jeremy Frey
- Content type: Research article
- Open Access
- Published: 10 July 2019
- Article: 48
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Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
Authors (first, second and last of 8)
- Lu Liang
- Chunfeng Ma
- Jianping Lin
- Content type: Software
- Open Access
- Published: 10 July 2019
- Article: 47
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Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery
Authors (first, second and last of 4)
- Munhwan Lee
- Hyeyeon Kim
- Hong-Gee Kim
- Content type: Research article
- Open Access
- Published: 09 July 2019
- Article: 46
This is part of 1 collection: -
Interoperable chemical structure search service
Authors
- Miroslav Kratochvíl
- Jiří Vondrášek
- Jakub Galgonek
- Content type: Software
- Open Access
- Published: 28 June 2019
- Article: 45
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Journal of Cheminformatics, ORCID, and GitHub
Authors
- Egon Willighagen
- Nina Jeliazkova
- Rajarshi Guha
- Content type: Editorial
- Open Access
- Published: 08 July 2019
- Article: 44
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Cheminformatics approach to exploring and modeling trait-associated metabolite profiles
Authors (first, second and last of 5)
- Jeremy R. Ash
- Melaine A. Kuenemann
- Denis Fourches
- Content type: Research article
- Open Access
- Published: 24 June 2019
- Article: 43
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Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
Authors (first, second and last of 7)
- Martin Pérez-Pérez
- Gael Pérez-Rodríguez
- Anália Lourenço
- Content type: Research article
- Open Access
- Published: 24 June 2019
- Article: 42
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KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images
Authors
- Isidro Cortés-Ciriano
- Andreas Bender
- Content type: Research article
- Open Access
- Published: 19 June 2019
- Article: 41
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DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Authors
- Eric W. Bell
- Yang Zhang
- Content type: Research article
- Open Access
- Published: 07 June 2019
- Article: 40
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Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis
Authors
- Inbal Tuvi-Arad
- Gil Alon
- Content type: Research article
- Open Access
- Published: 06 June 2019
- Article: 39
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An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
Authors (first, second and last of 4)
- Angela Serra
- Serli Önlü
- Dario Greco
- Content type: Research article
- Open Access
- Published: 06 June 2019
- Article: 38
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ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)
Authors (first, second and last of 5)
- Sebastian Fritsch
- Stefan Neumann
- Achim Zielesny
- Content type: Software
- Open Access
- Published: 04 June 2019
- Article: 37
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Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity
Authors (first, second and last of 4)
- Chad H. G. Allen
- Lewis H. Mervin
- Andreas Bender
- Content type: Research article
- Open Access
- Published: 31 May 2019
- Article: 36
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An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor
Authors (first, second and last of 5)
- Xuhan Liu
- Kai Ye
- Gerard J. P. van Westen
- Content type: Research article
- Open Access
- Published: 24 May 2019
- Article: 35
This is part of 1 collection: -
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening
Authors (first, second and last of 8)
- Patrick J. Ropp
- Jacob O. Spiegel
- Jacob D. Durrant
- Content type: Software
- Open Access
- Published: 24 May 2019
- Article: 34
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Capturing mixture composition: an open machine-readable format for representing mixed substances
Authors (first, second and last of 4)
- Alex M. Clark
- Leah R. McEwen
- Barry A. Bunin
- Content type: Research article
- Open Access
- Published: 23 May 2019
- Article: 33
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Bayesian optimization for conformer generation
Authors
- Lucian Chan
- Geoffrey R. Hutchison
- Garrett M. Morris
- Content type: Research article
- Open Access
- Published: 21 May 2019
- Article: 32
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Correction to: A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications
Authors (first, second and last of 4)
- Domenico Gadaleta
- Anna Lombardo
- Emilio Benfenati
- Content type: Correction
- Open Access
- Published: 25 April 2019
- Article: 31