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3 <title>MayaChemTools: References</title>
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11 </center>
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12 <br/>
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13 <h1>References</h1>
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14 <div class="References">
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15 <table width="100%" border="0" cellspacing="0" cellpadding="0">
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16 <tr><td width="30" align="right" valign="top">1.</td><td width="5"> </td><td align="left" valign="top">Wall, L.; Christiansen, T.; Schwartz, R.L. Programming Perl, 2nd edition. O'Reilly Media Inc., September 1996.</td></tr>
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17 <tr><td align="right" valign="top">2.</td><td> </td><td align="left" valign="top"><a href="http://www.cpan.org" title="Visit http://www.cpan.org">CPAN: Comprehensive Perl archive network.</a></td></tr>
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18 <tr><td align="right" valign="top">3.</td><td> </td><td align="left" valign="top"><a href="http://www.fsf.org" title="Visit http://www.fsf.org">FSF: Free software foundation.</a></td></tr>
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19 <tr><td align="right" valign="top">4.</td><td> </td><td align="left" valign="top">Knuth, D.E. The art of computer programming. Vol. 1-3. 2nd edition. Addison-Wesley, September 1998.</td></tr>
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20 <tr><td align="right" valign="top">5.</td><td> </td><td align="left" valign="top">Press, W.H.; Teukolsky, S.A.; Vetterling, W.T.; Flannery, B.P. Numerical recipies in C: the art of scientific computing. 2nd edition. Cambridge University Press, 1992.</td></tr>
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21 <tr><td align="right" valign="top">6.</td><td> </td><td align="left" valign="top">Orwant, J.; MacDonald, J.; Hietaniemi, J. Mastering algorithms with Perl. O'Reilly Media Inc., August 1999.</td></tr>
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22 <tr><td align="right" valign="top">7.</td><td> </td><td align="left" valign="top"><a href="http://www.webelements.com" title="Visit http://www.webelements.com">Data for elements in the periodic table.</a></td></tr>
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23 <tr><td align="right" valign="top">8.</td><td> </td><td align="left" valign="top"><a href="http://physics.nist.gov/PhysRefData/Compositions/index.html" title="Visit http://physics.nist.gov/PhysRefData/Compositions/index.html">Isotope data for elements in the periodic table.</a></td></tr>
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24 <tr><td align="right" valign="top">9.</td><td> </td><td align="left" valign="top"><a href="http://www.expasy.ch" title="Visit http://www.expasy.ch">Main data source for amino acids.</a></td></tr>
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25 <tr><td align="right" valign="top">10.</td><td> </td><td align="left" valign="top"><a href="http://www.perlmol.org" title="Visit http://www.perlmol.org">PerlMol - Perl modules for molecular chemistry.</a></td></tr>
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26 <tr><td align="right" valign="top">11.</td><td> </td><td align="left" valign="top"><a href="http://openbabel.sourceforge.net/wiki/Main_Page" title="Visit http://openbabel.sourceforge.net/wiki/Main_Page">OpenBabel: The open source chemistry toolbox.</a></td></tr>
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27 <tr><td align="right" valign="top">12.</td><td> </td><td align="left" valign="top"><a href="http://cdk.sourceforge.net" title="Visit http://cdk.sourceforge.net">CDK: The chemistry development kit.</a></td></tr>
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28 <tr><td align="right" valign="top">13.</td><td> </td><td align="left" valign="top"><a href="http://sourceforge.net/projects/joelib/" title="Visit http://sourceforge.net/projects/joelib/">JOELIB.</a></td></tr>
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29 <tr><td align="right" valign="top">14.</td><td> </td><td align="left" valign="top"><a href="http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php" title="Visit http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php">CTFile Formats.</a></td></tr>
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30 <tr><td align="right" valign="top">15.</td><td> </td><td align="left" valign="top">Conway, D. Object oriented Perl. 1st edition. O'Reilly Media Inc., January 2000.</td></tr>
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31 <tr><td align="right" valign="top">16.</td><td> </td><td align="left" valign="top">Friedl, J.E.F. Mastering regular expressions. 3rd edition. O'Reilly Media Inc., August 2006.</td></tr>
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32 <tr><td align="right" valign="top">17.</td><td> </td><td align="left" valign="top">Schulz, G.E.; Schirmer, R.H. Principles of protein structure. Springer-Verlag, January 1997.</td></tr>
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33 <tr><td align="right" valign="top">18.</td><td> </td><td align="left" valign="top">Saenger, W. Principles of nucleic acid structure. Springer-Verlag, 1983.</td></tr>
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34 <tr><td align="right" valign="top">19.</td><td> </td><td align="left" valign="top">Cornish-Bowden, A. Nomenclature for incompletely specified bases in nucleic acid sequence. Nucleic Acids Res. 1985, 13, 3021-3030.</td></tr>
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35 <tr><td align="right" valign="top">20.</td><td> </td><td align="left" valign="top">Clapham, C. A concise Oxford dictionary of mathematics. Oxford University Press, 1990.</td></tr>
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36 <tr><td align="right" valign="top">21.</td><td> </td><td align="left" valign="top">Cook, J.L. Conversion factors. Oxford University Press, 1993.</td></tr>
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37 <tr><td align="right" valign="top">22.</td><td> </td><td align="left" valign="top">Pauling, L. The nature of chemical bond. 3rd edition. Cornell University Press, June 1960.</td></tr>
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38 <tr><td align="right" valign="top">23.</td><td> </td><td align="left" valign="top"><a href="http://www.daylight.com/dayhtml/doc/theory/index.html" title="Visit http://www.daylight.com/dayhtml/doc/theory/index.html">Daylight theory manual.</a></td></tr>
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39 <tr><td align="right" valign="top">24.</td><td> </td><td align="left" valign="top">Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Am. Chem. Soc. 1988, 28, 31-36.</td></tr>
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40 <tr><td align="right" valign="top">25.</td><td> </td><td align="left" valign="top">Weininger, D.; Weininger, A.; Weininger, J.L. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Am. Chem. Soc. 1989, 29, 97-101.</td></tr>
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41 <tr><td align="right" valign="top">26.</td><td> </td><td align="left" valign="top">Weininger, D. SMILES. 3. Depit. Graphical depiction of chemical structures. J. Am. Chem. Soc. 1990, 30, 237-243.</td></tr>
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42 <tr><td align="right" valign="top">27.</td><td> </td><td align="left" valign="top"><a href="http://eyesopen.com/docs/toolkits/current/pdf/OEChem_TK-c++.pdf" title="Visit http://eyesopen.com/docs/toolkits/current/pdf/OEChem_TK-c++.pdf">OEChem TK manual.</a></td></tr>
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43 <tr><td align="right" valign="top">28.</td><td> </td><td align="left" valign="top">Parkin, G. Valence, oxidation number, and formal charge: Three related but fundamentally different concepts. J. Chem. Educ. 2006, 83, 791-799.</td></tr>
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44 <tr><td align="right" valign="top">29.</td><td> </td><td align="left" valign="top">Gateiger, J.; Jochum, C. An algorithm for the perception of synthetically important rigngs. J. Chem. Inf. Comput. Sci. 1979, 19, 43-47.</td></tr>
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45 <tr><td align="right" valign="top">30.</td><td> </td><td align="left" valign="top">Balducci, R.; Pearlman, R.S. Efficient exact solution of the ring perception problem. J. Chem. Inf. Comput. Sci. 1994, 34, 822-831.</td></tr>
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46 <tr><td align="right" valign="top">31.</td><td> </td><td align="left" valign="top">Hanser, T.; Jauffret, P.; Kaufmann, G. A new algorithm for exhaustive ring perception in a molecular graph. J. Chem. Inf. Comput. Sci. 1996, 36, 1146-1152.</td></tr>
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47 <tr><td align="right" valign="top">32.</td><td> </td><td align="left" valign="top">Cahn, R.S.; Ingold, C.; Prelog, V. Specification of molecular chirality. Angew. Chem. Internat. Edit. 1966, 5, 385-415.</td></tr>
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48 <tr><td align="right" valign="top">33.</td><td> </td><td align="left" valign="top">Prelog, V.; Helmchen, G. Basic principles of the CIP-system and proposals for revision. Angew. Chem. Internat. Edit. 1982, 21, 567-583.</td></tr>
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49 <tr><td align="right" valign="top">34.</td><td> </td><td align="left" valign="top">Mata, P.; Lobo, A.M.; Marshall, C.; Johnson, P.A. The CIP seqeunce rules: Analysis and proposal for a revision. Tetrahedron. 1993, 4, 657-668.</td></tr>
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50 <tr><td align="right" valign="top">35.</td><td> </td><td align="left" valign="top">Nourse, J.G.; Carhart, R.E.; Smith, D.H.; Djerassi, C. Exhaustive generation of stereoisomers for structure elucidation. J. Am. Chem. Soc. 1979, 101, 1216-1223.</td></tr>
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51 <tr><td align="right" valign="top">36.</td><td> </td><td align="left" valign="top">Nourse, J.G.; Smith, D.H.; Carhart, R.E.; Djerassi, C. Computer-assisted elucidation of molecular structue with stereochemistry. J. Am. Chem. Soc. 1980, 102, 6289-6295.</td></tr>
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52 <tr><td align="right" valign="top">37.</td><td> </td><td align="left" valign="top"><a href="http://www.chem.qmul.ac.uk/iupac/fusedring/" title="Visit http://www.chem.qmul.ac.uk/iupac/fusedring/">Fused ring systems.</a></td></tr>
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53 <tr><td align="right" valign="top">38.</td><td> </td><td align="left" valign="top"><a href="http://www.burtleburtle.net/bob/hash/doobs.html" title="Visit http://www.burtleburtle.net/bob/hash/doobs.html">A hash function for hash table lookup.</a></td></tr>
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54 <tr><td align="right" valign="top">39.</td><td> </td><td align="left" valign="top">Ralaivola, L.; Swamidass, S.J.; Saigo, H.; Baldi, P. Graph kernals for chemical informatics. Neural Networks. 2005, 18, 1093-1110.</td></tr>
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55 <tr><td align="right" valign="top">40.</td><td> </td><td align="left" valign="top">Willett. P.; Barnard, J.M.; Downs, G.M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.</td></tr>
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56 <tr><td align="right" valign="top">41.</td><td> </td><td align="left" valign="top">Holliday, J.D.; Hu, C-Y.; Willett, P. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings, Combinatorial Chemistry & High Throughput Screening. 2002, Vol. 5, No. 2, 155-166.</td></tr>
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57 <tr><td align="right" valign="top">42.</td><td> </td><td align="left" valign="top">Flinger, M.; Verducci, J.; Blower, P. A modification of the Jacard-Tanimoto similarity index for diverse selection of chemical compounds using binary strings. Technometrics. 2002, 44, 110-119.</td></tr>
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58 <tr><td align="right" valign="top">43.</td><td> </td><td align="left" valign="top">Wang, Y.; Bajorath, J. Balancing the influence of molecular complexity in fingerprint similarity searching. J. Chem. Inf. Comput. Sci. 2008, 48, 75-84.</td></tr>
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59 <tr><td align="right" valign="top">44.</td><td> </td><td align="left" valign="top">Flower, D.R. On the properties of bit string-based measures of chemical similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.</td></tr>
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60 <tr><td align="right" valign="top">45.</td><td> </td><td align="left" valign="top"><a href="http://accelrys.com/products/pdf/keys-to-keyset-technology.pdf" title="Visit http://accelrys.com/products/pdf/keys-to-keyset-technology.pdf">The Enkfil.dat and Eksfil.dat files: The keys to understanding MDL keyset technology.</a></td></tr>
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61 <tr><td align="right" valign="top">46.</td><td> </td><td align="left" valign="top">Durant, J.L.; Leland, B.A.; Henry, D.H.; Nourse, J.G. Reoptimization of MDL Keys for Use in Drug Discovery. J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280.</td></tr>
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62 <tr><td align="right" valign="top">47.</td><td> </td><td align="left" valign="top"><a href="https://list.indiana.edu/sympa/arc/chminf-l/2007-11/msg00058.html" title="Visit https://list.indiana.edu/sympa/arc/chminf-l/2007-11/msg00058.html">Description of public MACCS keys.</a></td></tr>
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63 <tr><td align="right" valign="top">48.</td><td> </td><td align="left" valign="top">Morgan, H.L. The generation of a unique machine description for chemical structures - A technique developed at chemical abstracts service. J. Chem. Doc. 1965, 5, 107-112.</td></tr>
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64 <tr><td align="right" valign="top">49.</td><td> </td><td align="left" valign="top">Penny, R.H. A connectivity code for use in describing chemical structures. J. Chem. Doc. 1965, 5, 113-117. J. Chem. Doc. 1973, 3, 153-157.</td></tr>
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65 <tr><td align="right" valign="top">50.</td><td> </td><td align="left" valign="top">Adamson, G.W.; Cowell, J.; Lynch, M.F.; McLure, A.H.; Town, W.G. Yapp, M. Strategic considerations in design of a screening system for substructure searches of chemical structure files.</td></tr>
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66 <tr><td align="right" valign="top">51.</td><td> </td><td align="left" valign="top">Wipke, W.T.; Krishnan, S.; Ouchi, G.I. Hash functions for rapid storage and retrieval of chemical structures. J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280. 1978, 18, 31- .</td></tr>
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67 <tr><td align="right" valign="top">52.</td><td> </td><td align="left" valign="top">Rogers, D.; Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Mod. 2010, 50, 742-754.</td></tr>
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68 <tr><td align="right" valign="top">53.</td><td> </td><td align="left" valign="top">Faulon, J.-L.; Visco, D.P., Jr.; Pophale, R.S. The Signature Molecular Descriptor. 1. Using extended valence sequences in QSAR and QSPR studies. J. Chem. Inf. Comput. Sci. 2003, 43, 707-720.</td></tr>
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69 <tr><td align="right" valign="top">54.</td><td> </td><td align="left" valign="top">Faulon, J.-L.; Collins, M.J.; Carr, R.D. The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences. J. Chem. Inf. Comput. Sci. 2004, 44, 427-436.</td></tr>
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70 <tr><td align="right" valign="top">55.</td><td> </td><td align="left" valign="top">Bender, A.; Mussa, H.Y.; Glen, R.C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.</td></tr>
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71 <tr><td align="right" valign="top">56.</td><td> </td><td align="left" valign="top">Bender, A.; Mussa, H.Y.; Glen, R.C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.</td></tr>
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72 <tr><td align="right" valign="top">57.</td><td> </td><td align="left" valign="top">Carhart, R.E.; Smith, D.H.; Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: Definition and application. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.</td></tr>
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73 <tr><td align="right" valign="top">58.</td><td> </td><td align="left" valign="top">Nilakantan, R.; Bauman, N.; Dixon, J.S.; Venkataraghavan, R. Topological torsion: A new molecular descriptor for SAR applications. Comparison with other descriptors. J. Chem. Inf. Comput. Sci. 1987, 27, 82-85.</td></tr>
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74 <tr><td align="right" valign="top">59.</td><td> </td><td align="left" valign="top">Langham, J.L.; Jain, A.N. Accurate and interpretable computational modeling of chemical mutagenicity. J. Chem. Inf. Comput. Sci. 2008, 48, 1833-1839.</td></tr>
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75 <tr><td align="right" valign="top">60.</td><td> </td><td align="left" valign="top">Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. Scaffold-hopping by topological pharmacophore search: A contribution to virtual screening. Angew. Chem. Int. Ed. 1999, 38, 2894-2896.</td></tr>
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76 <tr><td align="right" valign="top">61.</td><td> </td><td align="left" valign="top">Fechner, U.; Franke, L.; Renner, S.; Schneider, P. Schneider, G. Comparison of correlation vector methods for ligand-based similarity searching. J. Comput. Aided Mol. Des. 2003, 17, 687-698.</td></tr>
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77 <tr><td align="right" valign="top">62.</td><td> </td><td align="left" valign="top">Fechner, U.; Schneider, G. Evaluation of distance metrics for ligand-based similarity searching. ChemBioChem. 2004, 5, 538-540.</td></tr>
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78 <tr><td align="right" valign="top">63.</td><td> </td><td align="left" valign="top">Downs, G.M.; Willett, P.; Fisanick, W. Similarity searching and clustering of chemical-structure databases using molecular property data. J. Chem. Inf. Comput. Sci., 1994, 34, 1094-1102.</td></tr>
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79 <tr><td align="right" valign="top">64.</td><td> </td><td align="left" valign="top">Chen, X.; Reynolds, C.H.; Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients. J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414.</td></tr>
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80 <tr><td align="right" valign="top">65.</td><td> </td><td align="left" valign="top">Steffen, R.; Fechner, U.; Schneider, G. Alignment-free pharmacophore patterns: A correlation-vector approach. Pharmacophores and pharmacophore searches. 2006. Volume 32. Wiley-VCH. 49-80.</td></tr>
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81 <tr><td align="right" valign="top">66.</td><td> </td><td align="left" valign="top">McGregor, M.J.; Muskal, S. M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J. Chem. Inf. Comput. Sci. 1999, 39, 569-574.</td></tr>
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82 <tr><td align="right" valign="top">67.</td><td> </td><td align="left" valign="top">Floyd, R.W. Algorithm 97: Shortest path. Communications of the ACM. 1962, 5, 345.</td></tr>
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83 <tr><td align="right" valign="top">68.</td><td> </td><td align="left" valign="top">Horvath, D. Topological pharmacophores. Cheminformatics approaches to virtual screening. 2008. RSC Publishing. 44-75.</td></tr>
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84 <tr><td align="right" valign="top">69.</td><td> </td><td align="left" valign="top">Ewing, T.; Baber, C.; Feher, M. Novel 2D fingerprints in ligand-based virtual screening. J. Chem. Inf. Model. 2006, 46, 2423-2431.</td></tr>
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85 <tr><td align="right" valign="top">70.</td><td> </td><td align="left" valign="top">Watson, P. Naive Bayes classification using 2D pharmacophore feature triplet vectors. J. Chem. Inf. Model. 2008, 48, 166-178</td></tr>
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86 <tr><td align="right" valign="top">71.</td><td> </td><td align="left" valign="top">Bonachera, F.; Parent, B.; Barbosa, F.; Froloff, N.; Horvath, D. Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes. J. Chem. Inf. Model., 2006, 46, 2457-2477.</td></tr>
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87 <tr><td align="right" valign="top">72.</td><td> </td><td align="left" valign="top">Kearsley, S.K.; Sallamack, S.; Fluder, E.M.; Andose, J.D.; Mosley, R.T.; Sheridan, R.P. Chemical Similarity Using Physiochemical Property Descriptors.J. Chem. Inf. Comput. Sci., 1996, 36, 118-127.</td></tr>
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88 <tr><td align="right" valign="top">73.</td><td> </td><td align="left" valign="top">Filimonov, D.; Poroikov, V.; Borodina, Y.; Gloriozova, T. Chemical similarity assessment through multilevel neighborhoods of atoms: Definition and comparison with the other Descriptors. J. Chem. Inf. Comput. Sci., 1999, 39, 666-670.</td></tr>
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89 <tr><td align="right" valign="top">74.</td><td> </td><td align="left" valign="top"><a href="http://www.rdkit.org" title="Visit http://www.rdkit.org">RDKit - Cheminformatics and Machine Learning Software.</a></td></tr>
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90 <tr><td align="right" valign="top">75.</td><td> </td><td align="left" valign="top">Kier, L.B.; Hall, L.H. Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information. J. Chem. Inf. Comput. Sci. 1995, 35, 1039-1045.</td></tr>
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91 <tr><td align="right" valign="top">76.</td><td> </td><td align="left" valign="top">Kier, L.B.; Hall, L.H. Molecular structure description - The electrotopological state. Academic Press, 1999.</td></tr>
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92 <tr><td align="right" valign="top">77.</td><td> </td><td align="left" valign="top"><a href="http://www.edusoft-lc.com/molconn/" title="Visit http://www.edusoft-lc.com/molconn/">Molconn-Z - Program for generation of Molecular Connectivity, Shape, and Information Indices.</a></td></tr>
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93 <tr><td align="right" valign="top">78.</td><td> </td><td align="left" valign="top">Kier, L.B.; Hall, L.H. The E-State as the basis for molecular structure space definition and structure similarity. J. Chem. Inf. Comput. Sci. 2000, 40, 784-791.</td></tr>
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94 <tr><td align="right" valign="top">79.</td><td> </td><td align="left" valign="top"><a href="http://www.tripos.com/tripos_resources/fileroot/pdfs/mol2_format2.pdf" title="Visit http://www.tripos.com/tripos_resources/fileroot/pdfs/mol2_format2.pdf">SYBYL atom types.</a></td></tr>
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95 <tr><td align="right" valign="top">80.</td><td> </td><td align="left" valign="top">Clark, M.; Cramer III, R.D.; Opdenbosch, N.V. Validation of the general purpose Tripos 5.2 forcefield. J. Comput. Chem. 1989, 10, 982-1012.</td></tr>
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96 <tr><td align="right" valign="top">81.</td><td> </td><td align="left" valign="top">Rappe, A.K.; Casewit, C.J.; Colwell, K.S.; Goddard III, W.A.; Skiff, W.M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024-10035.</td></tr>
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97 <tr><td align="right" valign="top">82.</td><td> </td><td align="left" valign="top">Rappe, A. K. Personal communication. 2009.</td></tr>
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98 <tr><td align="right" valign="top">83.</td><td> </td><td align="left" valign="top">Halgren, T.A.; Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. 1996, J. Comput. Chem., 17, 490-519.</td></tr>
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99 <tr><td align="right" valign="top">84.</td><td> </td><td align="left" valign="top">Halgren, T.A.; Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J. Compt. Chem. 1996, 17, 520-552.</td></tr>
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142 <tr><td align="right" valign="top">125.</td><td> </td><td align="left" valign="top"><a href="http://www.rdkit.org/UGM/2012/Sayle_RDKitPerspective.pdf" title="Visit http://www.rdkit.org/UGM/2012/Sayle_RDKitPerspective.pdf">Sayle, R. Cheminformatics toolkits: A personal perspective.</a></td></tr>
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143 <tr><td align="right" valign="top">126.</td><td> </td><td align="left" valign="top"><a href="http://hop.perl.plover.com/" title="Visit http://hop.perl.plover.com/">Dominus, M. J. Higher-order Perl.</a></td></tr>
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144 <tr><td align="right" valign="top">127.</td><td> </td><td align="left" valign="top"><a href="http://www.opensmiles.org/opensmiles.pdf" title="Visit http://www.opensmiles.org/opensmiles.pdf">OpenSMILES.</a></td></tr>
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145 <tr><td align="right" valign="top">128.</td><td> </td><td align="left" valign="top"><a href="http://www.moldb.net/opensmarts/" title="Visit http://www.moldb.net/opensmarts/">Tim Vandermeersch. OpenSMARTS.</a></td></tr>
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146 </table>
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147 </div>
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