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Java Solutions for Cheminformatics

Java Solutions for Cheminformatics. March 2005. About Us. About Us Molecule Drawing and Visualization Structure Searching Cartridge Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments.

luke-boyer
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Java Solutions for Cheminformatics

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  1. Java Solutions for Cheminformatics March 2005

  2. About Us About Us Molecule Drawing and Visualization Structure Searching Cartridge Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  3. Formed: 1998 Budapest, Hungary Skills base: Chemistry, Software development, Predictive tools Aim: Platform independent software forchemistry Highlights 1998: Custom projects 1999: Java tools for sketching/viewing structures 2000: Structure database support 2001: Clustering and diversity analysis 2003: Pharmacophore screening, property predictions, reaction processing, fragmenting 2004: Cartridge technology, virtual synthesis, improved SMARTS support History

  4. People Developers: 17(7 Phd, 10 MSc) Technical expertise • Cheminformatics • Synthetic and physico-chemistry • Virtual drug design • Java • Web technology Business Support: 3(1 MSc, 2 BSc) Commercial expertise • Negotiation & contracting • Relationship management • Collaboration steering and development • Strategic marketing • Mutually benefitial (win win) business relationships

  5. Selected Application Areas Global licenses Custom development projects Value added constructions Websites/portal front and back end Educational

  6. Chemical drawing Product development 1998 1999 2000 2001 2002 2003 2004 Marvin SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3D rendering SMILES, SMARTS, PDB, Rgroups, isotopes, shortcuts, Marvin Beans Ball and stick, JPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning, (de)aromatization, reactions Partial charge, pKa, logP, logD, 3D generation, radicals, Sgroups Marvin file format, enhanced stereo, enhanced SMARTS support, shapes, text boxes, multiple groups, TPSA, Donor/Acceptor... Mac support, signed applets, Java Web Start, atom mapping Applets, Molfiles, stereo support, Windows, Unix JChem reaction searching, reaction processing, pharmacophoreanalysis. screening,standardization, fragmentation cartridge, enhanced stereo searching, recursive SMARTS, chemical expressions, virtual synthesis… clustering, diversity Oracle, MySQL, SQLServer, Access, hashed fingerprints, substructure and similarity searching DB2, PostgreSQL, Rgroup searching Structure Database and Cheminformatics toolkit

  7. Current Products Overview

  8. Multiple Deployment Formats • Applications • Java Applets • Signed Java Applets • Java Web Start • Java Beans • Plugins • JSP

  9. Why ChemAxon? • Sophisticated virtual chemistry technology • Platform independence and Web (Java) • High performance tools (speed, capacity) • Client oriented development • Comprehensive API for the developers • Detailed documentation • Competitive prices • Fast and reliable support

  10. Fast response to support question – max. 24 hourresponse (fast solution also!) Final and beta releases available online. Detailed documents available online and extensive help bundled within software Skilled and relevant human support quality (direct developer to developer) Product development based on support requests „Developers supporting developers” Product Support

  11. Molecule Drawing and Visualization About Us Molecule Drawing and Visualization Structure Searching Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  12. Operating Systems • 100% pure java • Windows • 95, 98, Me, NT, 2000, XP • Macintosh • OS 9, OS X • Unix • Linux, Solaris, Irix, etc.

  13. Web Browsers • Internet Explorer • Netscape • Mozilla • Safari • Opera

  14. Various file formats Isotopes, charges, radicals Alias, pseudo atoms Templates Abbreviated groups Reactions Atom maps R-groups Stereo bonds, stereo configurations (R/S, E/Z) Enhanced stereo(ABS/AND/OR) SMARTS properties (atoms, bonds, recursive SMARTS) Chemical errorchecking Generic atoms and bonds Atom lists and not lists 2D cleaning 3D cleaning Various 3D models Shapes, text boxes Plugins Marvin

  15. Various File Formats

  16. Isotopes, Charges, Radicals

  17. Templates

  18. Abbreviated Groups

  19. R-groups

  20. Reactions

  21. Rendered 3D displays with MarvinSpace

  22. Structure Cleaning CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 topology 2D 3D

  23. Structure Searching About Us Molecule Drawing and Visualization Structure Searching Cartridge Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  24. JChem Base Features • Rapid fingerprint-based database scanning • Sophisticated graph-based searching • Integration with databases • Oracle • MS SQL Server • DB2 • MYSQL • PostgreSQL • InterBase • Access • Custom standardization • JChem Cartridge for searching in Oracle • JSP integration

  25. Import with JChem Base Manager

  26. Exact structure Substructure Atom lists and notlists Explicit hydrogens Generic atoms Generic bonds SMARTS atom properties Aliphatic, aromatic Hydrogen count Connection count Valence Ring count Smallest ring size Recursive SMARTS Stereo atoms Stereo bonds R-group queries R-groups Occurence if / then conditions RestH Reaction search Transformation recognition Component identification Stereospecific reactions (inversion, retention) Diastereomers Enhanced stereo groups (Abs, And, Or) Query Features

  27. JChem Base JSP Integration Thin client support: only a web browser and Java required

  28. Cartridge Technology About Us Molecule Drawing and Visualization Structure Searching Cartridge Technology Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  29. JChem Cartridge for Oracle JChem Cartridge for Oracle Oracle can be extended to support chemical database operations using the JChem Cartridge for Oracle Examples: Substructure search displaying ID, SMILES codes, and molweight: SELECT cd_id, cd_smiles, cd_molweight FROM my_structuresWHERE jc_contains(cd_smiles, 'CC(=O)Oc1ccccc1C(O)=O') = 1; Finding benzene derivatives conforming the Lipinski’s rule of five: SELECT count(*) FROM my_structures WHERE jc_compare(structure, 'c1ccccc1','sep=!t:s!ctFilter:(mass() <= 500) &&(logP() <= 5) && (donorCount() <= 5) &&(acceptorCount() <= 10)') = 1;

  30. JChem Cartridge for Oracle JChem Cartridge for Oracle Example Oracle search returning similar structures with logP >1, which were acquired after April 14th, 2002. MarvinView below.

  31. Structure Standardization About Us Molecule Drawing and Visualization Structure Searching Cartridge Technology Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  32. Standardization • Explicit hydrogens • Aromatic bonds • Mesomers • Tautomers • Counterions

  33. Standardization Example before after

  34. Molecular Predictions About Us Molecule Drawing and Visualization Structure Searching Cartridge Technology Structure Standardization Molecular Predictions Chemical Expressions Screening Clustering Fragment Analysis Virtual Synthesis Current Developments

  35. Available Calculations Elemental analysis Charge distribution Polarizability pKa logP logD Polar surface area Huckel Analysis H-bond donor-acceptor Major microspecies Refractivity Calculation Interface Marvin GUI Command line Chemical Terms API Calculator Plugins

  36. Elemental Analysis

  37. Polar Surface Area

  38. Partial Charge Distribution

  39. Partial Charge Distribution Calculation Partial Equalization of Orbital Electronegativities (PEOE) Orbital electronegativity defined by Mulliken Orbital electronegativity of atom i: ci=at+btqi+ctqi2 qi: partial charge Partial charge of atom i is iteratively calculated based on Gasteiger’s method: ci(0)= at, qi(0)= 0 qi(n+1)= qi (n) + S(0.5)n(ci- ck)/ max(ci, ck) k: index of a neighbor of atom i

  40. Polarizability

  41. logP

  42. logP Example logP = Sfi fI: atomic logP increment

  43. Validation of the logP prediction

  44. logD

  45. logD Example 1+(1) 2+(2) 3-(3) k4 1+2+(4) 1+3-(5) 2+3-(6) k1 k7 k5 123(0) k2 1+2+3-(7) k6 k3 logD is computed using micro ionization constants (ki), micro partition coefficients (pi), and pH

  46. pKa

  47. pKa Plugin - Microconstants Micro ionization constants (logk) are calculated from regression equations that have three types of calculated parameters: Intramolecular interactions Partial charges logk Polarizabilities

  48. pKa Plugin - Macroconstants 1 3 2 Macro ionization constants (pKa) are calculated from the microconstants (logk) Ionization scheme 1- 1-2+ 123 2+ 1-3- 1-2+3- 3- 2+3-

  49. Hydrogen Bonds in pKa Calculation Dlogk = a (qi - qk) + b a,b:regression parameters Intramolecular hydrogen bonds are also taken into account

  50. Validation of the pKaprediction

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