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<article_title>Flexible 3D pharmacophores as descriptors of
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<journal_title>Journal of Molecular Graphics and
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<author>Jenkins</author>
<journal_title>Journal of medicinal
chemistry</journal_title>
<issue>25</issue>
<volume>47</volume>
<doi>10.1021/jm049654z</doi>
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Davies, J. W. (2004). A 3D similarity method for scaffold hopping from
known drugs or natural ligands to new chemotypes. Journal of Medicinal
Chemistry, 47(25), 6144–6159.
https://doi.org/10.1021/jm049654z</unstructured_citation>
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<journal_title>Scaffold hopping in medicinal
chemistry</journal_title>
<doi>10.1002/9783527665143.ch10</doi>
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<unstructured_citation>Jenkins, J. L. (2013). Feature point
pharmacophores (FEPOPS). Scaffold Hopping in Medicinal Chemistry,
155–174.
https://doi.org/10.1002/9783527665143.ch10</unstructured_citation>
</citation>
<citation key="ripphausen2011state">
<article_title>State-of-the-art in ligand-based virtual
screening</article_title>
<author>Ripphausen</author>
<journal_title>Drug discovery today</journal_title>
<issue>9-10</issue>
<volume>16</volume>
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Drug Discovery Today, 16(9-10), 372–376.
https://doi.org/10.1016/j.drudis.2011.02.011</unstructured_citation>
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<article_title>Principles of early drug
discovery</article_title>
<author>Hughes</author>
<journal_title>British journal of
pharmacology</journal_title>
<issue>6</issue>
<volume>162</volume>
<doi>10.1111/j.1476-5381.2010.01127.x</doi>
<cYear>2011</cYear>
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S. B., &amp; Philpott, K. L. (2011). Principles of early drug discovery.
British Journal of Pharmacology, 162(6), 1239–1249.
https://doi.org/10.1111/j.1476-5381.2010.01127.x</unstructured_citation>
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<issue>1</issue>
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Bender, A., &amp; Svozil, D. (2020). QSAR-derived affinity fingerprints
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Cheminformatics, 12(1), 41.
https://doi.org/10.1186/s13321-020-00444-5</unstructured_citation>
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<issue>1</issue>
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Journal of Medicinal Chemistry, 55(14), 6582–6594.
https://doi.org/10.1021/jm300687e</unstructured_citation>
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<article_title>K-means++ the advantages of careful
seeding</article_title>
<author>Arthur</author>
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<cYear>2007</cYear>
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(2007). K-means++ the advantages of careful seeding. Proceedings of the
Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1027–1035.
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applications</journal_title>
<issue>2</issue>
<volume>36</volume>
<doi>10.1016/j.eswa.2008.01.039</doi>
<cYear>2009</cYear>
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A simple and fast algorithm for k-medoids clustering. Expert Systems
with Applications, 36(2), 3336–3341.
https://doi.org/10.1016/j.eswa.2008.01.039</unstructured_citation>
</citation>
<citation key="gillet1998identification">
<article_title>Identification of biological activity
profiles using substructural analysis and genetic
algorithms</article_title>
<author>Gillet</author>
<journal_title>Journal of chemical information and computer
sciences</journal_title>
<issue>2</issue>
<volume>38</volume>
<doi>10.1021/ci970431+</doi>
<cYear>1998</cYear>
<unstructured_citation>Gillet, V. J., Willett, P., &amp;
Bradshaw, J. (1998). Identification of biological activity profiles
using substructural analysis and genetic algorithms. Journal of Chemical
Information and Computer Sciences, 38(2), 165–179.
https://doi.org/10.1021/ci970431+</unstructured_citation>
</citation>
<citation key="wildman1999prediction">
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<journal_title>Journal of chemical information and computer
sciences</journal_title>
<issue>5</issue>
<volume>39</volume>
<doi>10.1021/ci990307l</doi>
<cYear>1999</cYear>
<unstructured_citation>Wildman, S. A., &amp; Crippen, G. M.
(1999). Prediction of physicochemical parameters by atomic
contributions. Journal of Chemical Information and Computer Sciences,
39(5), 868–873.
https://doi.org/10.1021/ci990307l</unstructured_citation>
</citation>
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electronegativity—a rapid access to atomic charges</article_title>
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<journal_title>Tetrahedron</journal_title>
<issue>22</issue>
<volume>36</volume>
<doi>10.1016/0040-4020(80)80168-2</doi>
<cYear>1980</cYear>
<unstructured_citation>Gasteiger, J., &amp; Marsili, M.
(1980). Iterative partial equalization of orbital electronegativity—a
rapid access to atomic charges. Tetrahedron, 36(22), 3219–3228.
https://doi.org/10.1016/0040-4020(80)80168-2</unstructured_citation>
</citation>
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<article_title>An introduction to ROC
analysis</article_title>
<author>Fawcett</author>
<journal_title>Pattern recognition letters</journal_title>
<issue>8</issue>
<volume>27</volume>
<doi>10.1016/j.patrec.2005.10.010</doi>
<cYear>2006</cYear>
<unstructured_citation>Fawcett, T. (2006). An introduction
to ROC analysis. Pattern Recognition Letters, 27(8), 861–874.
https://doi.org/10.1016/j.patrec.2005.10.010</unstructured_citation>
</citation>
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