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  1. Software

    Molmil: a molecular viewer for the PDB and beyond

    We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan an...

    Gert-Jan Bekker, Haruki Nakamura and Akira R. Kinjo

    Journal of Cheminformatics 2016 8:42

    Published on: 26 August 2016

  2. Research article

    ILPC: simple chemometric tool supporting the design of ionic liquids

    Ionic liquids (ILs) found a variety of applications in today’s chemistry. Since their properties depend on the ions constituting particular ionic liquid, it is possible to synthetize IL with desired specificat...

    Maciej Barycki, Anita Sosnowska, Magdalena Piotrowska, Piotr Urbaszek, Anna Rybinska, Monika Grzonkowska and Tomasz Puzyn

    Journal of Cheminformatics 2016 8:40

    Published on: 19 August 2016

  3. Research article

    An activity canyon characterization of the pharmacological topography

    Highly chemically similar drugs usually possess similar biological activities, but sometimes, small changes in chemistry can result in a large difference in biological effects. Chemically similar drug pairs th...

    Varsha S. Kulkarni and David J. Wild

    Journal of Cheminformatics 2016 8:41

    Published on: 19 August 2016

  4. Research article

    Large-scale ligand-based predictive modelling using support vector machines

    The increasing size of datasets in drug discovery makes it challenging to build robust and accurate predictive models within a reasonable amount of time. In order to investigate the effect of dataset sizes on ...

    Jonathan Alvarsson, Samuel Lampa, Wesley Schaal, Claes Andersson, Jarl E. S. Wikberg and Ola Spjuth

    Journal of Cheminformatics 2016 8:39

    Published on: 10 August 2016

  5. Research article

    bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming

    Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algo...

    Jun Gao, Qingchen Zhang, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao and Ruixin Zhu

    Journal of Cheminformatics 2016 8:38

    Published on: 11 July 2016

  6. Software

    BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions

    More and more evidences from network biology indicate that most cellular components exert their functions through interactions with other cellular components, such as proteins, DNAs, RNAs and small molecules. ...

    Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hong-Yu Miao, Ai-Ping Lu, Wen-Bin Zeng and Dong-Sheng Cao

    Journal of Cheminformatics 2016 8:34

    Published on: 21 June 2016

  7. Database

    Literature information in PubChem: associations between PubChem records and scientific articles

    PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, l...

    Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Bo Yu, Benjamin A. Shoemaker, Jiyao Wang, Evan E. Bolton, Yanli Wang and Stephen H. Bryant

    Journal of Cheminformatics 2016 8:32

    Published on: 10 June 2016

  8. Software

    Advanced SPARQL querying in small molecule databases

    In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better...

    Jakub Galgonek, Tomáš Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz and Jiří Vondrášek

    Journal of Cheminformatics 2016 8:31

    Published on: 6 June 2016

  9. Research article

    Badapple: promiscuity patterns from noisy evidence

    Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer reliable knowledge from big and noisy data. ...

    Jeremy J. Yang, Oleg Ursu, Christopher A. Lipinski, Larry A. Sklar, Tudor I. Oprea and Cristian G. Bologa

    Journal of Cheminformatics 2016 8:29

    Published on: 28 May 2016

  10. Database

    Web-based 3D-visualization of the DrugBank chemical space

    Similarly to the periodic table for elements, chemical space offers an organizing principle for representing the diversity of organic molecules, usually in the form of multi-dimensional property spaces that ar...

    Mahendra Awale and Jean-Louis Reymond

    Journal of Cheminformatics 2016 8:25

    Published on: 4 May 2016

  11. Research article

    A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases

    Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, ...

    Ting Gao, Hongzhi Li, Wenze Li, Lin Li, Chao Fang, Hui Li, LiHong Hu, Yinghua Lu and Zhong-Min Su

    Journal of Cheminformatics 2016 8:24

    Published on: 3 May 2016

  12. Methodology

    Terminology spectrum analysis of natural-language chemical documents: term-like phrases retrieval routine

    This study seeks to develop, test and assess a methodology for automatic extraction of a complete set of ‘term-like phrases’ and to create a terminology spectrum from a collection of natural language PDF docum...

    Boris L. Alperin, Andrey O. Kuzmin, Ludmila Yu. Ilina, Vladimir D. Gusev, Natalia V. Salomatina and Valentin N. Parmon

    Journal of Cheminformatics 2016 8:22

    Published on: 29 April 2016

  13. Meeting abstracts

    11th German Conference on Chemoinformatics (GCC 2015)

    Uli Fechner, Chris de Graaf, Andrew E. Torda, Stefan Güssregen, Andreas Evers, Hans Matter, Gerhard Hessler, Nicola J. Richmond, Peter Schmidtke, Marwin H. S. Segler, Mark P. Waller, Stefanie Pleik, Joan-Emma Shea, Zachary Levine, Ryan Mullen, Karina van den Broek…

    Journal of Cheminformatics 2016 8(Suppl 1):18

    Published on: 26 April 2016

    This article is part of a Supplement: Volume 8 Supplement 1

  14. Research article

    Improving chemical similarity ensemble approach in target prediction

    In silico target prediction of compounds plays an important role in drug discovery. The chemical similarity ensemble approach (SEA) is a promising method, which has been successfully applied in many drug-relat...

    Zhonghua Wang, Lu Liang, Zheng Yin and Jianping Lin

    Journal of Cheminformatics 2016 8:20

    Published on: 23 April 2016

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