Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited

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This article has been cited by 63 ACS Journal articles (5 most recent appear below).

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  AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles

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  • AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles

    V. Lounnas and G. Vriend
    Journal of Chemical Information and Modeling2012 Article ASAP

    Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either ...

    Abstract | Full Text HTML | Hi-Res PDF | PDF w/ Links
• 

  Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical Cartridge

  Dimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev, Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger, Simson Alex, and Michael Farnum
  Journal of Chemical Information and Modeling2011 51 (12), 3113-3130

  • Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical Cartridge

    Dimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev, Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger, Simson Alex, and Michael Farnum
    Journal of Chemical Information and Modeling2011 51 (12), 3113-3130

    Efficient substructure searching is a key requirement for any chemical information management system. In this paper, we describe the substructure search capabilities of ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson ...

    Abstract | Full Text HTML | Hi-Res PDF | PDF w/ Links
• 

  Self-Contained Sequence Representation: Bridging the Gap between Bioinformatics and Cheminformatics

  William L. Chen, Burton A. Leland, Joseph L. Durant, David L. Grier, Bradley D. Christie, James G. Nourse, and Keith T. Taylor
  Journal of Chemical Information and Modeling2011 51 (9), 2186-2208

  • Self-Contained Sequence Representation: Bridging the Gap between Bioinformatics and Cheminformatics

    William L. Chen, Burton A. Leland, Joseph L. Durant, David L. Grier, Bradley D. Christie, James G. Nourse, and Keith T. Taylor
    Journal of Chemical Information and Modeling2011 51 (9), 2186-2208

    The wide application of next-generation sequencing has presented a new hurdle to bioinformatics for managing the fast-growing sequence data. The management of biomacromolecules at the chemistry level imposes an even greater challenge in cheminformatics ...

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  CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids

  Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, and Anthony J. Chubb
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  • CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids

    Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, and Anthony J. Chubb
    Journal of Chemical Information and Modeling2011 51 (4), 829-836

    We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features ...

    Abstract | Full Text HTML | Hi-Res PDF | PDF w/ Links
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  Intuitive Patent Markush Structure Visualization Tool for Medicinal Chemists

  Wei Deng, Steven J. Berthel, and W. Venus So
  Journal of Chemical Information and Modeling2011 51 (3), 511-520

  • Intuitive Patent Markush Structure Visualization Tool for Medicinal Chemists

    Wei Deng, Steven J. Berthel, and W. Venus So
    Journal of Chemical Information and Modeling2011 51 (3), 511-520

    A Markush, or generic structure, is a widely used convention in chemical and pharmaceutical patents. The flexibility and complexity of this format, however, preclude an easy understanding and analysis of chemical space. In this paper, an application ...

    Abstract | Full Text HTML | Hi-Res PDF | PDF w/ Links

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