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

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.

[1]  H. Wiener.  Correlation of Heats of Isomerization, and Differences in Heats of Vaporization of Isomers, Among the Paraffin Hydrocarbons , 1947 .

[2]  D. Cvetkovic,et al.  Graph theory and molecular orbitals , 1974 .

[3]  I. Gutman,et al.  Graph theory and molecular orbitals. XII. Acyclic polyenes , 1975 .

[4]  L B Kier,et al.  Molecular connectivity VII: specific treatment of heteroatoms. , 1976, Journal of pharmaceutical sciences.

[5]  Lemont B. Kier,et al.  A Shape Index from Molecular Graphs , 1985 .

[6]  L. Kier.  Shape Indexes of Orders One and Three from Molecular Graphs , 1986 .

[7]  S. Unger.  Molecular Connectivity in Structure–activity Analysis , 1987 .

[8]  Peter J. Rousseeuw,et al.  Finding Groups in Data: An Introduction to Cluster Analysis , 1990 .

[9]  Ali S. Hadi,et al.  Finding Groups in Data: An Introduction to Chster Analysis , 1991 .

[10]  Michel Petitjean,et al.  Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds , 1992, J. Chem. Inf. Comput. Sci..

[11]  Marina Lasagni,et al.  New molecular descriptors for 2D and 3D structures. Theory , 1994 .

[12]  Thomas A. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[13]  M. Karelson,et al.  Correlation of Boiling Points with Molecular Structure. 1. A Training Set of 298 Diverse Organics and a Test Set of 9 Simple Inorganics , 1996 .

[14]  Luhua Lai,et al.  A New Atom-Additive Method for Calculating Partition Coefficients , 1997, J. Chem. Inf. Comput. Sci..

[15]  Paola Gramatica,et al.  SD-modelling and Prediction by WHIM Descriptors. Part 5. Theory Development and Chemical Meaning of WHIM Descriptors , 1997 .

[16]  K. M. Smith,et al.  Novel software tools for chemical diversity , 1998 .

[17]  Robert S. Pearlman,et al.  Metric Validation and the Receptor-Relevant Subspace Concept , 1999, J. Chem. Inf. Comput. Sci..

[18]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , 1999, J. Chem. Inf. Comput. Sci..

[19]  Christoph Steinbeck,et al.  JChemPaint - Using the collaborative forces of the Internet to develop a free editor for 2D chemical structures , 2000 .

[20]  P. Selzer,et al.  Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. , 2000, Journal of medicinal chemistry.

[21]  Henry S. Rzepa,et al.  Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM , 2001, J. Chem. Inf. Comput. Sci..

[22]  Christoph Steinbeck,et al.  SENECA: A Platform-Independent, Distributed, and Parallel System for Computer-Assisted Structure Elucidation in Organic Chemistry , 2001, J. Chem. Inf. Comput. Sci..

[23]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[24]  Johann Gasteiger,et al.  Prediction of 1H NMR chemical shifts using neural networks. , 2002, Analytical chemistry.

[25]  Eugene Russo.  Chemistry plans a structural overhaul , 2002, Nature.

[26]  Christoph Steinbeck,et al.  NMRShiftDB-Constructing a Free Chemical Information System with Open-Source Components , 2003, J. Chem. Inf. Comput. Sci..

[27]  J. Meiler.  PROSHIFT: Protein chemical shift prediction using artificial neural networks , 2003, Journal of biomolecular NMR.

[28]  Egon L. Willighagen,et al.  The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics , 2003, J. Chem. Inf. Comput. Sci..

[29]  Renate Kania,et al.  Classification of Chemical Compounds to Support Complex Queries in a Pathway Database , 2004, Comparative and functional genomics.

[30]  Egon L. Willighagen,et al.  Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , 2004, J. Chem. Inf. Model..

[31]  Christoph Steinbeck,et al.  NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. , 2004, Phytochemistry.

[32]  Henry S. Rzepa,et al.  JUMBO - An XML infrastructure for eScience , 2004 .

[33]  Rajarshi Guha.  Using the CDK as a backend to R , 2005 .

[34]  Using R to provide statistical functionality for QSAR modeling in CDK A description of the integration of CDK and the R statistical environment , 2005 .