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  1. Content type: Software

    Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, an...

    Authors: Dominique Sydow, Andrea Morger, Maximilian Driller and Andrea Volkamer

    Citation: Journal of Cheminformatics 2019 11:29

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  2. Content type: Research article

    Because drug–drug interactions (DDIs) may cause adverse drug reactions or contribute to complex-disease treatments, it is important to identify DDIs before multiple-drug medications are prescribed. As the alte...

    Authors: Jian-Yu Shi, Kui-Tao Mao, Hui Yu and Siu-Ming Yiu

    Citation: Journal of Cheminformatics 2019 11:28

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  3. Content type: Methodology

    Several QSAR methodology developments have shown promise in recent years. These include the consensus approach to generate the final prediction of a model, utilizing new, advanced machine learning algorithms a...

    Authors: Kristijan Vukovic, Domenico Gadaleta and Emilio Benfenati

    Citation: Journal of Cheminformatics 2019 11:27

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  4. Content type: Research article

    The process of ligand binding to a biological target can be represented as the equilibrium between the relevant solvated and bound states of the ligand. This which is the basis of structure-based, rigorous met...

    Authors: Willem Jespers, Mauricio Esguerra, Johan Åqvist and Hugo Gutiérrez-de-Terán

    Citation: Journal of Cheminformatics 2019 11:26

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  5. Content type: Research article

    Random peptide libraries that cover large search spaces are often used for the discovery of new binders, even when the target is unknown. To ensure an accurate population representation, there is a tendency to...

    Authors: Daniela Kalafatovic, Goran Mauša, Toni Todorovski and Ernest Giralt

    Citation: Journal of Cheminformatics 2019 11:25

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  6. Content type: Research article

    Docking is commonly used in drug discovery to predict how ligand binds to protein target. Best programs are generally able to generate a correct solution, yet often fail to identify it. In the case of drug-lik...

    Authors: Célien Jacquemard, Malgorzata N. Drwal, Jérémy Desaphy and Esther Kellenberger

    Citation: Journal of Cheminformatics 2019 11:24

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  7. Content type: Research article

    Scientific research is increasingly characterised by the volume of documents and data that it produces, from experimental plans and raw data to reports and papers. Researchers frequently struggle to manage and...

    Authors: Samantha Kanza, Nicholas Gibbins and Jeremy G. Frey

    Citation: Journal of Cheminformatics 2019 11:23

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  8. Content type: Research article

    Efficient representations of drugs provide important support for healthcare analytics, such as drug–drug interaction (DDI) prediction and drug–drug similarity (DDS) computation. However, incomplete annotated d...

    Authors: Ying Shen, Kaiqi Yuan, Min Yang, Buzhou Tang, Yaliang Li, Nan Du and Kai Lei

    Citation: Journal of Cheminformatics 2019 11:22

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  9. Content type: Research article

    Recent applications of recurrent neural networks (RNN) enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the enum...

    Authors: Josep Arús-Pous, Thomas Blaschke, Silas Ulander, Jean-Louis Reymond, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2019 11:20

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  10. Content type: Database

    Drug discovery typically involves investigation of a set of compounds (e.g. drug screening hits) in terms of target, disease, and bioactivity. CSgator is a comprehensive analytic tool for set-wise interpretati...

    Authors: Sera Park, Yeajee Kwon, Hyesoo Jung, Sukyung Jang, Haeseung Lee and Wankyu Kim

    Citation: Journal of Cheminformatics 2019 11:17

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  11. Content type: Review

    Mass spectrometry imaging (MSI) using laser ablation (LA) inductively coupled plasma (ICP) is an innovative and exciting methodology to perform highly sensitive elemental analyses. LA-ICP-MSI of metals, trace ...

    Authors: Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim and Robert Winkler

    Citation: Journal of Cheminformatics 2019 11:16

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  12. Content type: Research

    Sodium-dependent glucose co-transporter 1 (SGLT1) is a solute carrier responsible for active glucose absorption. SGLT1 is present in both the renal tubules and small intestine. In contrast, the closely related...

    Authors: Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2019 11:15

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  13. Content type: Software

    Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researche...

    Authors: Patrick J. Ropp, Jesse C. Kaminsky, Sara Yablonski and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2019 11:14

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  14. Content type: Research article

    Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioa...

    Authors: Emma Ricart, Valérie Leclère, Areski Flissi, Markus Mueller, Maude Pupin and Frédérique Lisacek

    Citation: Journal of Cheminformatics 2019 11:13

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  15. Content type: Research article

    OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structura...

    Authors: Francois Berenger, Kam Y. J. Zhang and Yoshihiro Yamanishi

    Citation: Journal of Cheminformatics 2019 11:10

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  16. Content type: Research article

    In this paper, we explore the impact of combining different in silico prediction approaches and data sources on the predictive performance of the resulting system. We use inhibition of the hERG ion channel tar...

    Authors: Thierry Hanser, Fabian P. Steinmetz, Jeffrey Plante, Friedrich Rippmann and Mireille Krier

    Citation: Journal of Cheminformatics 2019 11:9

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  17. Content type: Research article

    Ligand efficiency is a widely used design parameter in drug discovery. It is calculated by scaling affinity by molecular size and has a nontrivial dependency on the concentration unit used to express affinity ...

    Authors: Peter W. Kenny

    Citation: Journal of Cheminformatics 2019 11:8

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  18. Content type: Research article

    We present a text-mining tool for recognizing biomedical entities in scientific literature. OGER++ is a hybrid system for named entity recognition and concept recognition (linking), which combines a dictionary...

    Authors: Lenz Furrer, Anna Jancso, Nicola Colic and Fabio Rinaldi

    Citation: Journal of Cheminformatics 2019 11:7

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  19. Content type: Preliminary communication

    To facilitate the development of new nanomaterials, especially nanomedicines, a novel computational approach was developed to precisely predict the hydrophobicity of gold nanoparticles (GNPs). The core of this...

    Authors: Wenyi Wang, Xiliang Yan, Linlin Zhao, Daniel P. Russo, Shenqing Wang, Yin Liu, Alexander Sedykh, Xiaoli Zhao, Bing Yan and Hao Zhu

    Citation: Journal of Cheminformatics 2019 11:6

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  20. Content type: Research article

    Biogenic compounds are important materials for drug discovery and chemical biology. In this work, we report a quasi-biogenic molecule generator (QBMG) to compose virtual quasi-biogenic compound libraries by me...

    Authors: Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu and Jun Xu

    Citation: Journal of Cheminformatics 2019 11:5

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  21. Content type: Research article

    Structure–activity relationship modelling is frequently used in the early stage of drug discovery to assess the activity of a compound on one or several targets, and can also be used to assess the interaction ...

    Authors: Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey and Andrew R. Leach

    Citation: Journal of Cheminformatics 2019 11:4

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  22. Content type: Software

    A number of computational tools for metabolism prediction have been developed over the last 20 years to predict the structures of small molecules undergoing biological transformation or environmental degradati...

    Authors: Yannick Djoumbou-Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach and David S. Wishart

    Citation: Journal of Cheminformatics 2019 11:2

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  23. Content type: Software

    The need for synthetic route design arises frequently in discovery-oriented chemistry organizations. While traditionally finding solutions to this problem has been the domain of human experts, several computat...

    Authors: Ian A. Watson, Jibo Wang and Christos A. Nicolaou

    Citation: Journal of Cheminformatics 2019 11:1

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  24. Content type: Research article

    The need to efficiently find and extract information from the continuously growing biomedical literature has led to the development of various annotation tools aimed at identifying mentions of entities and rel...

    Authors: Sérgio Matos

    Citation: Journal of Cheminformatics 2018 10:68

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  25. Content type: Meeting report

    The Computational Chemistry List is a mailing list, portal, and community which brings together people interested in computational chemistry, mostly practitioners. It was formed in 1991 and continues to exist ...

    Authors: Frédéric Wieber, Alejandro Pisanty and Alexandre Hocquet

    Citation: Journal of Cheminformatics 2018 10:67

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  26. Content type: Research article

    Among the various molecular fingerprints available to describe small organic molecules, extended connectivity fingerprint, up to four bonds (ECFP4) performs best in benchmarking drug analog recovery studies as...

    Authors: Daniel Probst and Jean-Louis Reymond

    Citation: Journal of Cheminformatics 2018 10:66

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  27. Content type: Research article

    In biomedical research, patents contain the significant amount of information, and biomedical text mining has received much attention in patents recently. To accelerate the development of biomedical text minin...

    Authors: Ling Luo, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Jian Wang and Hongfei Lin

    Citation: Journal of Cheminformatics 2018 10:65

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  28. Content type: Research article

    The large number of chemical and pharmaceutical patents has attracted researchers doing biomedical text mining to extract valuable information such as chemicals, genes and gene products. To facilitate gene and...

    Authors: Po-Ting Lai, Ming-Siang Huang, Ting-Hao Yang, Wen-Lian Hsu and Richard Tzong-Han Tsai

    Citation: Journal of Cheminformatics 2018 10:64

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  29. Content type: Research article

    Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and ...

    Authors: Johannes Kirschnick, Philippe Thomas, Roland Roller and Leonhard Hennig

    Citation: Journal of Cheminformatics 2018 10:63

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  30. Content type: Methodology

    Protein-ligand docking programs are routinely used in structure-based drug design to find the optimal binding pose of a ligand in the protein’s active site. These programs are also used to identify potential d...

    Authors: Hio Kuan Tai, Siti Azma Jusoh and Shirley W. I. Siu

    Citation: Journal of Cheminformatics 2018 10:62

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  31. Content type: Research article

    The partition coefficient between octanol and water (logP) has been an important descriptor in QSAR predictions for many years and therefore the prediction of logP has been examined countless times. One of the...

    Authors: Jeffrey Plante and Stephane Werner

    Citation: Journal of Cheminformatics 2018 10:61

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  32. Content type: Research article

    The quality of data used for QSAR model derivation is extremely important as it strongly affects the final robustness and predictive power of the model. Ambiguous or wrong structures need to be carefully check...

    Authors: Domenico Gadaleta, Anna Lombardo, Cosimo Toma and Emilio Benfenati

    Citation: Journal of Cheminformatics 2018 10:60

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  33. Content type: Software

    The goal of chemmodlab is to streamline the fitting and assessment pipeline for many machine learning models in R, making it easy for researchers to compare the utility of these models. While focused on implem...

    Authors: Jeremy R. Ash and Jacqueline M. Hughes-Oliver

    Citation: Journal of Cheminformatics 2018 10:57

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  34. Content type: Research article

    Current ligand-based machine learning methods in virtual screening rely heavily on molecular fingerprinting for preprocessing, i.e., explicit description of ligands’ structural and physicochemical properties i...

    Authors: Raghuram Srinivas, Pavel V. Klimovich and Eric C. Larson

    Citation: Journal of Cheminformatics 2018 10:56

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  35. Content type: Methodology

    Simplified representation of compound databases has several applications in cheminformatics. Herein, we introduce an alternative and general method to build single fingerprint representations of compound datab...

    Authors: Norberto Sánchez-Cruz and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2018 10:55

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  36. Content type: Research article

    Topological data analysis is a family of recent mathematical techniques seeking to understand the ‘shape’ of data, and has been used to understand the structure of the descriptor space produced from a standard...

    Authors: Mariam Pirashvili, Lee Steinberg, Francisco Belchi Guillamon, Mahesan Niranjan, Jeremy G. Frey and Jacek Brodzki

    Citation: Journal of Cheminformatics 2018 10:54

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  37. Content type: Research article

    When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typicall...

    Authors: Yasemin Yesiltepe, Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Mark I. Borkum, Patrick N. Reardon, Nancy M. Washton, Thomas O. Metz, Justin G. Teeguarden, Niranjan Govind and Ryan S. Renslow

    Citation: Journal of Cheminformatics 2018 10:52

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  38. Content type: Research article

    Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statis...

    Authors: César R. García-Jacas, Lisset Cabrera-Leyva, Yovani Marrero-Ponce, José Suárez-Lezcano, Fernando Cortés-Guzmán, Mario Pupo-Meriño and Ricardo Vivas-Reyes

    Citation: Journal of Cheminformatics 2018 10:51

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  39. Content type: Research article

    Fast and accurate identification of potential drug candidates against therapeutic targets (i.e., drug–target interactions, DTIs) is a fundamental step in the early drug discovery process. However, experimental...

    Authors: Ming Hao, Stephen H. Bryant and Yanli Wang

    Citation: Journal of Cheminformatics 2018 10:50

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  40. Content type: Research article

    Ligand-based predictive modeling is widely used to generate predictive models aiding decision making in e.g. drug discovery projects. With growing data sets and requirements on low modeling time comes the nece...

    Authors: Alexander Kensert, Jonathan Alvarsson, Ulf Norinder and Ola Spjuth

    Citation: Journal of Cheminformatics 2018 10:49

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