References

Many of the references in this book contain a URL. These are listed here to make them easy to locate.

• Chapter 2
  • U. S. Environmental Protection Agency. 2007. Estimation Program Interface (EPI) suite. http://www.epa.gov/oppt/exposure/pubs/episuite.htm
• Chapter 3
  • PostgreSQL 8.2 documentation, 2008. Dblink. http://www.postgresql.org/docs/current/static/dblink.html
• Chapter 4
  • Fermilab Computing Division. 2005. Comparison of Oracle, MySQL and PostgreSQL DBMS. http://www-css.fnal.gov/dsg/external/freeware/mysql-vs-pgsql.html
  • O’Donnell, T.J. 2005. CHORD extension to PostgreSQL. http://www.gnova.com
  • Schmid, E. 2004. Pgchem::tigress extension to PostgreSQL. http://pgfoundry.org/projects/pgchem
  • Landrum, G. 2006. RDKit: Cheminformatics and Machine Learning Software. http://rdkit.sourceforge.net/
  • Daycart. 2008. http://www.daylight.com; Jchem cartridge. http://www.chemaxon.com; CambridgeSoft Oracle cartridge. http://www.cambridgesoft.com; MDL Isentris. http://www.symyx.com
  • Kumar, T. 2005. Small molecules database cartridge. http://www.unm.edu/~tharun/smdb.html
  • PostgreSQL 8.2 documentation. 2008. C-language functions. http://www.postgresql.org/docs/8.2/static/xfunc-c.html
• Chapter 5
  • PhpPgAdmin. http://www.phppgadmin.com
  • PhpMyAdmin. http://www.phpmyadmin.net/
  • PgAdminIII. http://www.pgadmin.org
  • Oracle SQL developer. http://www.oracle.com/technology/products/database/sql_developer/index.html
  • Toad DBA suite for Oracle. http://www.quest.com/Toad-DBA-Suite-for-Oracle/
  • The R project for statistical computing. http://www.r-project.org
  • RODBC database interface module. http://cran.r-project.org/web/packages/RODBC/index.html
  • Spotfire. http://spotfire.tibco.com/products/decisionsite.cfm
  • SciTegic Platform. http://www.accelrys.com/products/scitegic/
  • Perl DBI module. http://search.cpan.org/~timb/DBI/DBI.pm
  • PyGreSQL – PostgreSQL module for Python. http://www.pygresql.org
  • PyGreSQL Programming Information. http://www.pygresql.org/pg.html
  • Oracle OCI8 Functions. http://www.php.net/oci
  • PHP PostgreSQL Functions. http://www.php.net/pgsql
• Chapter 6
  • PubChem Compounds. http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound
  • PubChem Text Search. http://pubchem.ncbi.nlm.nih.gov/
  • PubChem BioAssay. http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay
  • PhpPgAdmin. http://phppgadmin.sourceforge.net/
  • O'Boyle, N., 2007. Pybel - Hack that SD file. http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html
  • O’Donnell, T. J., 2008. Sdf2sql program. http://www.gnova.com/software.html
  • Materialized Views. http://snapshot.projects.postgresql.org/
• Chapter 7
  • Sdf molfiles. http://en.wikipedia.org/wiki/MDL_Molfile
  • PDB files. http://www.wwpdb.org/docs.html
  • O’Donnell, T.J., 2008. CHORD. http://www.gnova.com/
  • Daylight Oracle Cartridge. http://daylight.com/products/daycart.html
  • O'Shea, M. D., 2008. Chemistry data cartridges. http://www.strychnine.co.uk/oracledatacartridges.html
  • SMARTS tutorial. http://daylight.com/dayhtml/doc/theory/index.html
  • Sayle, R., and G. Skillman, 2002. Hooked on protonics.
    http://www.eyesopen.com/about/events/presentations/acs02/tsld018.htm
  • Sayle, R., and Delany, J. 1999. Canonicalization and enumeration of tautomers. http://www.daylight.com/meetings/emug99/Delany/taut_html/index.htm
  • Chemaxon. Calculator plugins. http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html#tautomer
  • ScienceServe. Tautomer. http://www.scienceserve.com/Software/molnet/tautomer/index.htm
• Chapter 8
  • Hash function. http://en.wikipedia.org/wiki/Hash_function
  • Fingerprints, chapter 6. http://daylight.com/dayhtml/doc/theory/index.html
• Chapter 9
  • SMIRKS tutorial, 2007. http://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html
• Chapter 10
  • Plpgsql, 2008. http://www.postgresql.org/docs/8.2/static/plpgsql.html
  • Tubert-Brohman, I., PerlMol, 2006. http://www.perlmol.org
  • Kelley, B., FROWNS, 2002. http://frowns.sourceforge.net/
  • OpenBabel, 2008. http://openbabel.sourceforge.net/
  • O’Donnell, T.J., CHORD, 2008. http://www.gnova.com/
  • Pgchem. http://pgfoundry.org/projects/pgchem/
  • Grimes, S., 1998. Modeling object/relational databases. http://www.dbmsmag.com/9804d13.html
  • Object-relational database. http://en.wikipedia.org/wiki/Object-relational_database
  • Devarakonda, R. S., 2001. Object-relational database systems - The road ahead. http://www.acm.org/crossroads/xrds7-3/ordbms.html
• Chapter 11
  • OpenBabel. http://openbabel.sourceforge.net/
  • QSAR datasets. http://www.qsarworld.com/
  • VLA4 dataset. http://www.qsarworld.com/qsar-datasets-porter.php
• Chapter 12
  • Perl DBI. http://search.cpan.org/~timb/DBI/DBI.pm#fetchall_arrayref
  • R project. http://cran.r-project.org/manuals.html
• Chapter 13
  • PubChem. http://pubchem.ncbi.nlm.nih.gov/
  • Marvin. http://www.chemaxon.com/
  • Pubchem. ftp://ftp.ncbi.nih.gov/pubchem/
• Appendix
  • PostgreSQL documentation. Plperl. http://www.postgresql.org/docs/8.0/interactive/plperl-trusted.html
  • Kelley, B. FROWNS, 2002. http://frowns.sourceforge.net/
  • Dalke, A. PyDaylight, 2000. http://www.daylight.com/meetings/mug00/Dalke/index.html
  • OpenBabel. http://openbabel.org/wiki/Main_Page
  • PubChem. http://pubchem.ncbi.nlm.nih.gov/
  • Porter, J., 2003. VLA4 dataset. http://www.qsarworld.com/qsar-datasets-porter.php
  • National Cancer Institute. NCI compounds. http://cactus.nci.nih.gov/ncidb2/download.html