Literature DB >> 16796559

Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

Christoph Steinbeck1, Christian Hoppe, Stefan Kuhn, Matteo Floris, Rajarshi Guha, Egon L Willighagen.   

Abstract

The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.

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Year:  2006        PMID: 16796559     DOI: 10.2174/138161206777585274

Source DB:  PubMed          Journal:  Curr Pharm Des        ISSN: 1381-6128            Impact factor:   3.116


  147 in total

1.  DemQSAR: predicting human volume of distribution and clearance of drugs.

Authors:  Ozgur Demir-Kavuk; Jörg Bentzien; Ingo Muegge; Ernst-Walter Knapp
Journal:  J Comput Aided Mol Des       Date:  2011-11-20       Impact factor: 3.686

2.  Chemical space: missing pieces in cheminformatics.

Authors:  Sean Ekins; Rishi R Gupta; Eric Gifford; Barry A Bunin; Chris L Waller
Journal:  Pharm Res       Date:  2010-08-04       Impact factor: 4.200

3.  Finding metabolic pathways using atom tracking.

Authors:  Allison P Heath; George N Bennett; Lydia E Kavraki
Journal:  Bioinformatics       Date:  2010-04-25       Impact factor: 6.937

4.  Large-scale elucidation of drug response pathways in humans.

Authors:  Yael Silberberg; Assaf Gottlieb; Martin Kupiec; Eytan Ruppin; Roded Sharan
Journal:  J Comput Biol       Date:  2012-02       Impact factor: 1.479

5.  Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS.

Authors:  Emma L Schymanski; Michael Gerlich; Christoph Ruttkies; Steffen Neumann
Journal:  Mass Spectrom (Tokyo)       Date:  2014-08-16

Review 6.  A cheminformatic toolkit for mining biomedical knowledge.

Authors:  Gus R Rosania; Gordon Crippen; Peter Woolf; David States; Kerby Shedden
Journal:  Pharm Res       Date:  2007-03-24       Impact factor: 4.200

7.  ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr.

Authors:  John Overington
Journal:  J Comput Aided Mol Des       Date:  2009-02-05       Impact factor: 3.686

8.  The great descriptor melting pot: mixing descriptors for the common good of QSAR models.

Authors:  Yufeng J Tseng; Anton J Hopfinger; Emilio Xavier Esposito
Journal:  J Comput Aided Mol Des       Date:  2011-12-27       Impact factor: 3.686

9.  MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures.

Authors:  Lochana C Menikarachchi; Shannon Cawley; Dennis W Hill; L Mark Hall; Lowell Hall; Steven Lai; Janine Wilder; David F Grant
Journal:  Anal Chem       Date:  2012-10-23       Impact factor: 6.986

10.  Drug target predictions based on heterogeneous graph inference.

Authors:  Wenhui Wang; Sen Yang; Jing Li
Journal:  Pac Symp Biocomput       Date:  2013
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