Software tools for chemical and scientific informatics

1
Software tools forchemical and scientific
informatics

• David Wild
• Visiting Assistant Professor
• School of Informatics
• djwild_at_indiana.edu

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Software at IUB Informatics

• Spotfire DecisionSite
• Chemistry / molecular modeling applications
• ChemTK, ArgusLab, MOE
• BCI software cluster analysis
• OpenEye software docking
• Chemaxon
• Chemoinformatics programming toolkits
• Daylight, BCI, OpenEye

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Spotfire DecisionSite

• Scientific Visualization software for analyzing
  large amounts of data
• Excellent Swedish design!
• Very high amount of functionality, tailored to
  life sciences industries
• We currently have a 20-seat license at Indiana,
  some still available

4
Charles Minard, 1861
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ChemTK

• Windows program for organizing and doing simple
  analysis on chemical datasets
• Free lite version can handle 250 structures,
  available for download from www.sageinformatics.co
  m
• We have license for full version, which can
  handle 1m structures

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ArgusLab

• Free molecular modeling program, downloadable
  from http//www.planaria-software.com/
• Has been extensively evaluated at Indiana
• Good 3D molecular visualization capability with a
  surprising amount of built-in functionality (e.g.
  docking)
• Some robustness problems and rough edges

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MOE

• Molecular Operating Environment
• Molecular modeling tool, with flexible scripting
  language
• See www.chemcomp.com

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BCI Software

• Cluster analysis (Wards, Divisive K-means,
  K-means)
• Designed for chemistry fingerprints, but can be
  used on any bitstring or numeric data
• Fingerprint generation
• Custom chemical fragment dictionaries
• Markush structure handling
• Enumeration, non-enumerative profiling and
  selection
• See www.bci.gb.com

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Comparative execution timesNCI subsets, 2.2 GHz
Intel Celeron processor
7h 27m
3h 06m
2h 25m
44m
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Clustering a 1 million compound dataseton a 2.2
GHz Celeron Desktop Machine
Time for a single run may vary due to
different selection of seeds. Runtimes can be
shortened e.g. by using a max. number of
iterations or a relocation cutoff.
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OpenEye Software

• OMEGA
• Generation of 3D conformers from 2D structures
• FRED
• Very fast docking of structures to proteins
• Other programs available, see www.eyesopen.com

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ChemAxon / JChem

• Set of modules
• Marvin is a collection of Java tools for drawing,
  displaying and characterizing chemical
  structures, substructures and reactions.
• JChem Baseadds a chemical interface to corporate
  databases, which can be applied for combined SQL
  and structural queriesimports/exports
  molecules, substructures, or reactions in
  standard formats (Molfile, SD file, RD file,
  SMILES, SMARTS, etc.).
• JChem Cartridgeadds chemical knowledge to the
  Oracle platform giving automatic access to
  Oracle's security, scalability, and replication
  features.
• Standardizerstructure canonization tool
  converting molecules from different formats into
  standard representation.
• Screenscreening based on pharmacophore or
  chemical fingerprints or other descriptors.
• Reactorgenerating reaction products from reaction
  equations and reactants.
• Fragmentergenerating building blocks based on
  Recap rules from molecule libraries.
• Serial Molecule Generatortransforming molecules
  by a sequence of user-defined transformations.
• Chemical Term Evaluatorevaluating chemical
  expressions.
• JKlustorclustering and diversity calculations
  based on molecular fingerprints or other
  properties.
• See www.chemaxon.com and www.jchem.com

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Chemistry Toolkits

• A toolkit is an interface to pre-written routines
  that perform chemistry-related tasks
• Provides chemistry objects, e.g.
• Molecule, atom, dataset, cluster, fingerprint
• And functions to work on these objects, e.g.
• Convert SMILES to molecule object
• Delete atom from a molecule
• Cluster a dataset
• Calculate tanimoto similarity between fingerprints

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Commercial Toolkits Available

• Daylight Toolkit (2D)
• http//www.daylight.com/products/
• http//www.daylight.com/meetings/summerschool00/co
  urse/toolkit/ for examples
• Fingerprints, SMILES, SMARTS, reaction, database
• Available on Unix platforms
• BCI Toolkit (2D)
• http//www.bci.gb.com
• Fingerprints, clustering, Markush
• Available on Unix and Windows platforms

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Commercial Toolkits Available

• OpenEye OEChem (2D/3D)
• http//www.eyesopen.com/oechem/
• Wide range of 2D and 3D functionality
• Available for Windows / Unix / Mac

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Example 1

• include ltstdio.hgt
• include dt_smiles.h
• main()
• char smiles200
• dt_Handle mol
• printf(Enter SMILES String )
• fscanf(stdin,s,smiles)
• mol dt_smilin(strlen(smiles), smiles)
• printf(\nMolecule has d atoms.\n,
• dt_count(mol, TYP_ATOM))

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Example 2

• include ltstdio.hgt
• include dt_smiles.h
• include dt_smarts.h
• main()
• char smiles200, smarts200
• dt_Handle mol,sub
• printf(Enter SMILES String )
• fscanf(stdin,s,smiles)
• printf(Enter SMARTS String )
• fscanf(stdin,s,smarts)
• mol dt_smilin(strlen(smiles), smiles)
• sub dt_smartin(strlen(smarts), smarts)
• if(dt_match(sub, mol, 1) ! NULL_OB)
• printf(SMARTS substructure is contained
  within the SMILES structure\n)

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More information on using the Daylight Toolkit

• Daylight is installed on xavier.informatics.indana
  .edu
• Look in DY_ROOT/contrib/src/c for example source
  code and makefiles
• Easiest way is to copy an existing makefile (e.g.
  in the DY_ROOT/contrib/src/c/smiles directory)
  and modify for any libraries / source code you
  need
• See Daylight website at www.daylight.com,
  especially support documentation