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  1. UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based ...

    Authors: Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa Bellis, Shaun McGlinchey and John P Overington
    Citation: Journal of Cheminformatics 2013 5:3
  2. Mycobacterium tuberculosis encodes 11 putative serine-threonine proteins Kinases (STPK) which regulates transcription, cell development and interaction with the host cells. From the 11 STPKs three kinases name...

    Authors: Abhik Seal, Perumal Yogeeswari, Dharmaranjan Sriram, OSDD Consortium and David J Wild
    Citation: Journal of Cheminformatics 2013 5:2
  3. PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived...

    Authors: Sunghwan Kim, Evan E Bolton and Stephen H Bryant
    Citation: Journal of Cheminformatics 2013 5:1
  4. Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound ...

    Authors: Claudia Bobach, Timo Böhme, Ulf Laube, Anett Püschel and Lutz Weber
    Citation: Journal of Cheminformatics 2012 4:40
  5. InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of I...

    Authors: Igor Pletnev, Andrey Erin, Alan McNaught, Kirill Blinov, Dmitrii Tchekhovskoi and Steve Heller
    Citation: Journal of Cheminformatics 2012 4:39
  6. Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in ...

    Authors: Stefan Höck and Rainer Riedl
    Citation: Journal of Cheminformatics 2012 4:38
  7. Exchange of chemical structures between practicing chemists is essential to chemical communication. The International Chemical Identifier (InChI) provides a means for lossless communication of structures witho...

    Authors: Steven M Bachrach
    Citation: Journal of Cheminformatics 2012 4:34
  8. The International Chemical Identifier (InChI) has had a dramatic impact on providing a means by which to deduplicate, validate and link together chemical compounds and related information across databases. Its...

    Authors: Antony J Williams
    Citation: Journal of Cheminformatics 2012 4:33
  9. In this work, we analyzed and compared the distribution profiles of a wide variety of molecular properties for three compound classes: drug-like compounds in MDL Drug Data Report (MDDR), non-drug-like compound...

    Authors: Mingyun Shen, Sheng Tian, Youyong Li, Qian Li, Xiaojie Xu, Junmei Wang and Tingjun Hou
    Citation: Journal of Cheminformatics 2012 4:31
  10. To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-...

    Authors: Sunghwan Kim, Evan E Bolton and Stephen H Bryant
    Citation: Journal of Cheminformatics 2012 4:28
  11. Assigning bond orders is a necessary and essential step for characterizing a chemical structure correctly in force field based simulations. Several methods have been developed to do this. They all have advanta...

    Authors: Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Liling Zhang and Tingjun Hou
    Citation: Journal of Cheminformatics 2012 4:26
  12. HSQC spectra are routinely acquired for chemical structure analysis based on hydrogen and carbon chemical environments. Two fast HSQC peak matching algorithms have been developed; a nearest neighbour approach ...

    Authors: Gregory K Pierens, Steven Brossi, Zhengyi Yang, David C Reutens and Viktor Vegh
    Citation: Journal of Cheminformatics 2012 4:25
  13. Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Gen...

    Authors: Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon and Thomas Hankemeier
    Citation: Journal of Cheminformatics 2012 4:21
  14. High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screen...

    Authors: Vincent Le Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer and Luc Morin-Allory
    Citation: Journal of Cheminformatics 2012 4:20
  15. With the exponential increase in the number of available ligand-receptor complexes, researchers are becoming more dedicated to mine these complexes to facilitate the drug design and development process. Theref...

    Authors: Raed Khashan
    Citation: Journal of Cheminformatics 2012 4:18
  16. The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related area...

    Authors: Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison
    Citation: Journal of Cheminformatics 2012 4:17
  17. MicroRNAs (miRNA) are small endogenously transcribed regulatory RNA which modulates gene expression at a post transcriptional level. These small RNAs have now been shown to be critical regulators in a number o...

    Authors: Salma Jamal, Vinita Periwal, OpenSourceDrugDiscovery Consortium and Vinod Scaria
    Citation: Journal of Cheminformatics 2012 4:16
  18. This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (C...

    Authors: Weerapong Phadungsukanan, Markus Kraft, Joe A Townsend and Peter Murray-Rust
    Citation: Journal of Cheminformatics 2012 4:15
  19. The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science’). We invited people who shared our vision for the potential of the web to support chemica...

    Authors: Peter Murray-Rust and Henry S Rzepa
    Citation: Journal of Cheminformatics 2012 4:14
  20. Small molecule chemistry is of central importance to a number of R&D companies in diverse areas such as the pharmaceutical, nutraceutical, food flavoring, and cosmeceutical industries. In order to store and ma...

    Authors: Elyette Martin, Aurélien Monge, Jacques-Antoine Duret, Federico Gualandi, Manuel C Peitsch and Pavel Pospisil
    Citation: Journal of Cheminformatics 2012 4:11
  21. Terms representing chemical concepts found the Unified Medical Language System (UMLS) are used to derive an expanded semantic network with mutually exclusive semantic types. The UMLS Semantic Network (SN) is c...

    Authors: C Paul Morrey, Yehoshua Perl, Michael Halper, Ling Chen and Huanying “Helen” Gu
    Citation: Journal of Cheminformatics 2012 4:9
  22. Authors: Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Ines dos Santos Vieira, Gregor Fels, Sandra Gesing, Richard Grunzke, Sonja Herres-Pawlis, Oliver Kohlbacher, Jens Krüger, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Patrick Schäfer, Thomas Steinke…
    Citation: Journal of Cheminformatics 2012 4(Suppl 1):P21

    This article is part of a Supplement: Volume 4 Supplement 1