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      <bibtex:note>Several articles (for example "The Cathedral and the Bazaar",
          "Homesteading the Noosphere") on the foundations of the open-source idea,
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          can be found on http://www.tuxedo.org/. Further, http://www.opensource.org/
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  <bibtex:entry id="PMR99">
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      <bibtex:author>Murray-Rust, P. and Rzepa, H.S.</bibtex:author>
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      <bibtex:volume>39</bibtex:volume>
      <bibtex:number>6</bibtex:number>
      <bibtex:pages>928-942</bibtex:pages>
      <bibtex:abstract>Chemical markup language (CML) is an application of XML, the
          extensible markup language, developed for containing chemical information
          components within documents.Its design supports interoperability with the XML
          family of tools and protocols.It provides a base functionality for atomic,
          molecular, and crystallographic information and allows extensibility for other
          chemical applications.Legacy files can be imported into CML without information
          loss and can carry any desired chemical ontology.Some applications of CML
          (Markush structures, chemical searching) will be discussed in later articles.An
          XML document type declaration (DTD) for CML is included as a
          Chart.</bibtex:abstract>
      <bibtex:keywords>information</bibtex:keywords>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="PMR2003">
    <bibtex:article>
      <bibtex:author>Murray-Rust, P. and Rzepa, H.S.</bibtex:author>
      <bibtex:title>Chemical Markup, XML, and the World Wide Web. 4. CML Schema</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer
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    </bibtex:article>
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  <bibtex:entry id="PMR2002">
    <bibtex:misc>
      <bibtex:author>Murray-Rust, P. and Rzepa, H.S.</bibtex:author>
      <bibtex:title>STMML. A MARKUP LANGUAGE FOR SCIENTIFIC, TECHNICAL AND MEDICAL PUBLISHING</bibtex:title>
      <bibtex:url>http://www.ch.ic.ac.uk/rzepa/codata2/</bibtex:url>
    </bibtex:misc>
  </bibtex:entry>

  <bibtex:entry id="RZEPA04">
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      <bibtex:author>Murray-Rust, P. and Rzepa, H.S. and Williamson, M.J. and Willighagen, E.L.</bibtex:author>
      <bibtex:title>Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators</bibtex:title>
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    </bibtex:article>
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  <bibtex:entry id="SMILESTUT">
    <bibtex:misc>
      <bibtex:title>SMILES Tutorial</bibtex:title>
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    </bibtex:misc>
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  <bibtex:entry id="SSMILESTUT">
    <bibtex:misc>
      <bibtex:title>SSMILES Tutorial</bibtex:title>
      <bibtex:url>http://www.daylight.com/dayhtml/smiles/ssmiles.html</bibtex:url>
    </bibtex:misc>
  </bibtex:entry>
  
  <bibtex:entry id="SCH84">
    <bibtex:article>
      <bibtex:author>Von Scholley, A.</bibtex:author>
      <bibtex:title></bibtex:title>
      <bibtex:journal>J. Chem. Inf. Comput. Sci.</bibtex:journal>
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  </bibtex:entry>

  <bibtex:entry id="STE2001">
    <bibtex:article>
      <bibtex:author>Steinbeck, C.</bibtex:author>
      <bibtex:title>SENECA: A platform-independent, distributed, and parallel system
          for computer-assisted structure elucidation in organic chemistry</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer Sciences</bibtex:journal>
      <bibtex:year>2001</bibtex:year>
      <bibtex:volume>41</bibtex:volume>
      <bibtex:number>6</bibtex:number>
      <bibtex:pages>1500-1507</bibtex:pages>
      <bibtex:abstract>The program package SENECA for Computer-Assisted Structure
          Elucidation (CASE) of organic molecules is described.SENECA is written
          completely in the programming language Java and divided into a server, a client,
          and a gatekeeper part.While the client allows for input of spectroscopic
          information, the server part performs the actual structure elucidation by
          stochastically walking through constitution space while optimizing the molecule
          toward agreement with given spectral properties.The convergence is guided by
          simulated annealing.The gatekeeper administers a list of server processes, which
          can be retrieved by the client.The package is completely platform-independent
          and its server part can be distributed over the Internet or an intranet using a
          heterogeneous network of almost any number and type of computers, thus allowing
          for parallel CASE computations on ordinary networks, present in almost any
          institution.[References: 23]</bibtex:abstract>
      <bibtex:doi>10.1021/ci000407n</bibtex:doi>
      <bibtex:keywords>Chemical-structure,Natural-products,Spectroscopy,Molecules,Search.,
          Chemistry in Current Contents(R)/Physical, Chemical and Earth,Sciences.</bibtex:keywords>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="STE2002">
    <bibtex:article>
      <bibtex:author>Steinbeck, C. and Kuhn, S. and Krause, S.</bibtex:author>
      <bibtex:title>NMRShiftDB - Constructing a Chemical Information System with Open Source Components</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer Sciences</bibtex:journal>
      <bibtex:year>2002</bibtex:year>
      <bibtex:volume>43</bibtex:volume>
      <bibtex:number>6</bibtex:number>
      <bibtex:doi>10.1021/ci0341363</bibtex:doi>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="STE2003">
    <bibtex:article>
      <bibtex:author>Steinbeck, C. and Han, Y. and Kuhn, S, and Horlacher, O. and Luttmann, E. and Willighagen, E.</bibtex:author>
      <bibtex:title>The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer Sciences</bibtex:journal>
      <bibtex:year>2003</bibtex:year>
      <bibtex:volume>43</bibtex:volume>
      <bibtex:pages>493-500</bibtex:pages>
      <bibtex:doi>10.1021/ci025584y</bibtex:doi>
      <bibtex:url>http://www.cdk.org/</bibtex:url>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="TOD98">
    <bibtex:article>
      <bibtex:author>Todeschini, R. and Gramatica, P.</bibtex:author>
      <bibtex:title>New 3D Molecular Descriptors: The WHIM theory and QAR Applications</bibtex:title>
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      <bibtex:pages>355-380</bibtex:pages>
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  </bibtex:entry>

  <bibtex:entry id="TRI92">
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      <bibtex:title>Chemical Graph Theory</bibtex:title>
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      <bibtex:isbn>0-8493-4256-2</bibtex:isbn>
    </bibtex:book>
  </bibtex:entry>

  <bibtex:entry id="WANG00">
    <bibtex:article>
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        <bibtex:title>Calculating partition coefficient by atom-additive method</bibtex:title>
      <bibtex:journal>Perspectives in Drug Discovery and Design</bibtex:journal>
      <bibtex:year>2000</bibtex:year>
      <bibtex:volume>19</bibtex:volume>
      <bibtex:pages>47-66</bibtex:pages>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="WANG97">
    <bibtex:article>
        <bibtex:author>Wang, R., Fu, Y., and Lai, L.</bibtex:author>
        <bibtex:title>A New Atom-Additive Method for Calculating Partition Coefficients</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer
          Sciences</bibtex:journal>
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      <bibtex:author>Weininger, David</bibtex:author>
      <bibtex:title>SMILES, a Chemical Language and Information System. 1.
          Introduction to Methodology and Encoding Rules</bibtex:title>
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  <bibtex:entry id="WEI89">
    <bibtex:article>
      <bibtex:author>Weininger, David and Weininger, Arthur and Weininger, Joseph
        L.</bibtex:author>
      <bibtex:title>SMILES 2. Algorithm for Generation of Unique SMILES
          Notation</bibtex:title>
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          Sciences</bibtex:journal>
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   <bibtex:entry id="SHA97">
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        <bibtex:author>
            Sharma, V. and Goswami, R. and Madan, A.K.
      </bibtex:author>
      <bibtex:title>
          Eccentric Connectivity Index: A Novel Highly Discriminating
          Topological Descriptor for Structure-Property and
          Structure-Activity Studies
          </bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer
          Sciences</bibtex:journal>
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      <bibtex:volume>37</bibtex:volume>
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        </bibtex:author>
        <bibtex:title>Prediction of Human Intestinal Absorption of Drug Compounds
        From Molecular Structure</bibtex:title>
      <bibtex:journal>Journal of Chemical Information and Computer
          Sciences</bibtex:journal>
      <bibtex:year>1998</bibtex:year>
      <bibtex:volume>38</bibtex:volume>
      <bibtex:pages>726-735</bibtex:pages>
    </bibtex:article>
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  <bibtex:entry id="STA90">
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        <bibtex:author>Stanton, D.T. and Jurs, P.C.
        </bibtex:author>
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        <bibtex:title>LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins</bibtex:title>
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      <bibtex:volume>15</bibtex:volume>
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        <bibtex:title>The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume
        and to Dot Surface Contourin gof Molecular Assemblies</bibtex:title>
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    <bibtex:article>
      <bibtex:author>Willighagen, E.L.</bibtex:author>
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      <bibtex:journal>Internet Journal of Chemistry</bibtex:journal>
      <bibtex:year>2001</bibtex:year>
      <bibtex:volume>4</bibtex:volume>
      <bibtex:abstract>
        This article describes the first opensource Java implementation of import 
        filters for the Chemical Markup Language (CML). The filters support CML conventions 
        and were tested with two opensource project: Jmol, a 3D molecular viewer, and
        JChemPaint, a chemical editor. Furthermore, the use of conventions in CML is 
        explained and the reason for using conventions is pointed out. Finally, the 
        implementation is compared with two recently developed techniques for handling 
        CML data.
      </bibtex:abstract>
      <bibtex:keywords>XML, CML, Java</bibtex:keywords>
    </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="XML">
      <bibtex:misc>
          <bibtex:author>World Wide Web Consortium</bibtex:author>
          <bibtex:title>Extensible Markup Language (XML) 1.0</bibtex:title>
          <bibtex:month>Feb</bibtex:month>
          <bibtex:year>1998</bibtex:year>
          <bibtex:url>http://www.w3.org/TR/1998/REC-xml-19980210</bibtex:url>
      </bibtex:misc>
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      <bibtex:article>
          <bibtex:author>  Petitjean, M.
          </bibtex:author>
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          <bibtex:author> Bath, P.A. and Poirette, A.R. and Willet, P. and Allen, F.H.
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          <bibtex:title>The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape Coefficients of Chemical Compounds</bibtex:title>
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          <bibtex:pages>714-716</bibtex:pages>
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          </bibtex:author>
          <bibtex:title>On molecular identification numbers  </bibtex:title>
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          <bibtex:author>Bemis, G.W. and Murcko, M.A.
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          <bibtex:volume>39</bibtex:volume>
          <bibtex:pages>2887-2893</bibtex:pages>
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          <bibtex:author>Breneman, C.M. and Thompson, T.R. and Rhem, M. and Dung, M.
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          <bibtex:title> Electron Density Modeling of Large Systems Using the Transferable Atom Equivalent Method </bibtex:title>
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      <bibtex:article>
          <bibtex:author>Breneman, C.M. and Rhem, M.
          </bibtex:author>
          <bibtex:title>A QSPR Analysis of HPLC Column Capacity
Factors for a set of High-Energy Materials Using Electronic Van der Waals
Surface Property Descriptors Computed by the Transferable Atom Equivalent 
Method </bibtex:title>
          <bibtex:journal>Journal of Computational Chemistry</bibtex:journal>
          <bibtex:year>1997</bibtex:year>
          <bibtex:volume>18</bibtex:volume>
          <bibtex:pages>182-197</bibtex:pages>
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  <bibtex:entry id="WHITE2003">
      <bibtex:article>
          <bibtex:author>Whitehead, C.E. and Sukumar, N. and Breneman, C.M. and Ryan, M.D.
          </bibtex:author>
          <bibtex:title> Transferable Atom Equivalent Multi-Centered Multipole Expansion Method</bibtex:title>
          <bibtex:journal>Journal of Computational Chemistry</bibtex:journal>
          <bibtex:year>2003</bibtex:year>
          <bibtex:volume>24</bibtex:volume>
          <bibtex:pages>512-529</bibtex:pages>
      </bibtex:article>
  </bibtex:entry>

  <bibtex:entry id="LIU98">
      <bibtex:article>
          <bibtex:author>Liu, S. and Cao, C. and Li, Z.
          </bibtex:author>
          <bibtex:title>Approach to Estimation and Prediction for Normal
                Boiling Point (NBP) of Alkanes Based on a Novel Molecular
                      Distance Edge (MDE) Vector, lambda</bibtex:title>
          <bibtex:journal>Journal of Chemical Information and Computer Sciences</bibtex:journal>
          <bibtex:year>1998</bibtex:year>
          <bibtex:volume>38</bibtex:volume>
          <bibtex:pages>387-394</bibtex:pages>
      </bibtex:article>
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  <bibtex:entry id="BALL2007">
      <bibtex:article>
          <bibtex:author>Bellester, P.J. and Richards, W.G.
          </bibtex:author>
          <bibtex:title>Ultrafast shape recognition to search compound databases for similar molecular shapes</bibtex:title>
          <bibtex:journal>Journal of Computational Chemistry</bibtex:journal>
          <bibtex:year>2007</bibtex:year>
          <bibtex:volume></bibtex:volume>
          <bibtex:pages></bibtex:pages>
      </bibtex:article>
  </bibtex:entry>

</bibtex:file>
