Marvin. Sketching, viewing and predicting properties with Marvin - features, tips and tricks. Gyorgy Pirok. Solutions for Cheminformatics

Transcription

1 Marvin Sketching, viewing and predicting properties with Marvin - features, tips and tricks Gyorgy Pirok Solutions for Cheminformatics

2 The Marvin family The Marvin toolkit provides web-enabled components for displaying and drawing chemical structures. MarvinSketch MarvinView MarvinSpace molecule, query, reaction and Markush drawing visualization of structure sets small and macromolecule visualization in 3D

3 Marvin Main features Main technical features New features 5.0 Features coming 5.1 Future features 5.2 Calculator Plugins

4 Isotopes, charges, radicals

5 Stereo features

6 Valence check, lone pairs

7 Alias, pseudo, attached data

8 Rich formatting

9 Any atom, atom list, link nodes

10 Atom properties

11 Bond and reaction topology

12 Recursive SMARTS

13 Markush structure drawing

14 Abbreviated groups

15 Component autorecognition

16 Map numbers and automapping

17 Electron flow arrows

18 2D and 3D clean CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 2D 3D

19 Aromatization/dearomatization

20 Multipage documents

21 Molecule matrix view 21

22 Marvin Main features Main technical features New features 5.0 Features coming 5.1 Future features 5.2 Calculator Plugins

23 File formats

24 Image export

25 3D in MarvinView and MarvinSpace MarvinView MarvinSpace

26 Beans vs. Applets Desktop applications (deployment with Installer, Java Web Start) Recommended for end-users Easy installation Recommended for developers Quick GUI building Easy customization Marvin integration into web pages Wide range of layout customization Recommended for web developers Simple web base deployment Modular architecture ensures short download time

27 Windows 95, 98, Me, NT, 2000, XP Mac OS X Unix/Linux Linux, Solaris, etc. System compatibility

28 Browser compatibility Internet Explorer Firefox Mozilla Netscape Safari Opera

29 Developing with Marvin Beans Use Marvin Beans to add MarvinSketch or MarvinView as a components in your standalone application. Additional API is available for Import / Export Performing calculations with plugins 2D and 3D cleaning of structures All operations accessible in the GUIs are also available in the API.

30 Applet specific features The appropriate version for the browser / JRE is automatically selected Signed (trusted) applets enable access to local files, system clipboard and allow printing. Applet API accessible from JavaScript to fetch the current structure from the applet and send it to the server for further processing. change the structure or display options of the applet without reloading the page.

31 Marvin Main features Main technical features New features 5.0 Features coming 5.1 Future features 5.2 Calculator Plugins

32 New, flexible user interface

33 Customizable menu and toolbar

34 OLE component

35 Query tab

36 IUPAC names

37 Spreadsheet view

38 Multicenters, coordinate bonds

39 Marvin Main features Main technical features New features 5.0 New features 5.1 Future features 5.2 Calculator Plugins

40 New features 5.1 Accelerated initialization of Marvin at startup Name to structure conversion Importing IUPAC names through the source On the fly conversion of names pasted to the canvas Opening.name files Printing redesign Print preview Print to PDF Structure preview (optional) on the file open dialog window Browsing capability in multi-structure files

41 Structure preview

42 Marvin Main features Main technical features New features 5.0 Future features 5.1 Future features 5.2 Calculator Plugins

43 Transparent structure drawing Future features 5.2 Multistep reaction support with automatic assignment of reaction components MarvinView GUI redesign Structure checker component Copy/Cut/Paste/Drag&Drop redesign CDX (ChemDraw) file import/export Load templates from specified directories New Markush related features Enhanced handling of group attachment points Dynamic font size change

44 Main original features Main original technical features New features 5.0 New features 5.1 Future features 5.2 Calculator Plugins Calculator Plugins

45 Marvin plugins Elemental Analysis IUPAC Naming Protonation pk a, Major Microspecies, Isoelectric Point Partitioning logp, logd Charge Charge, Polarizability, Orbital Electronegativity Isomers Tautomers, Resonance, Stereoisomers Conformation Conformers, Molecular Dynamics Geometry Topology Analysis, Geometry, Polar Surface Area, Molecular Surface Area Markush enumeration Other H Bond Donor/Acceptor, Huckel Analysis, Refractivity

46 Where to use Calculator Plugins? Drug development (QSAR, drug-likeness) Database filtering (lead-likeness) Reaction optimization/modelling Enumeration of Markush libraries (patents, combinatorial library)

47 Elemental Analysis Basic descriptors New features dot-disconnected isotope formula deuterium and tritium as D and T Customizable elemental and isotopic masses

48 IUPAC naming IUPAC name generation according to the latest provisional IUPAC specification No limitations (number of rings, size of the molecule) Growing traditional name dictionary New feature: name-tostructure

49 Protonation Plugin Bundle Calculates the acidic and basic pk a of protonizable groups Handles C-H acidity Adjustable range ph dependent microspecies distribution graph Major Microspecies Isoelectric Point

50 Calculation of logp and logd Partitioning Plugin Bundle

51 Charge Plugin Bundle Partial charge distribution 3D surface visualization Resonant structure distinction Polarizability Orbital Electronegativity

52 Isomers Plugin Bundle: Tautomers Calculates all tautomeric forms Predicts dominant tautomers (ph dependent) Canonical tautomeric structure

53 Isomers Plugin Bundle: Resonance All resonant structures Filtering the most relevant mesomers Canonical resonants

54 Isomers Plugin Bundle: Stereoisomers Tetrahedral stereo isomers Double bond stereo isomers Invalid 3D filter

55 Conformation Plugin Bundle Conformers Calculates different energy level conformers Lowest energy conformer selection Intramolecular H bond visualization Molecular Dynamics

56 Geometry Plugin Bundle: Topology Analysis Ring and ring system functions Path based functions Distance based functions Stereo functions Topological indexes

57 Geometry Plugin Bundle Topology Analysis Ring and ring system functions Path based functions Distance based functions Stereo functions Topological indexes Geometry Dreiding energy Steric hindrance Polar Surface Area Molecular Surface Area Van der Waals Solvent accessible

58 Markush Enumeration Options Library size calculation Sequential enumeration Random enumeration modes Valence filter option to discard chemically unacceptable results Coloring and alignment Features Atom lists Generic bonds Link nodes R-groups Variable position ligands

59 HBDA Hydrogen bond donor and acceptor functions for small and macromolecules Microspecies distribution graph

60 Future improvements Name-to-structure IUPAC naming, extensive traditional name dictionary Trainable pk a Improved logp calculations Faster conformation generation Shape descriptors in Topology Analysis

61 MarvinSketch and MarvinView Command line How to use Plugins? Chemical Terms ( language for the combination of property calculations) Search filters (drug-likeness, bioavailability, ) Virtual reaction rules Pharmacophore mapping Goal functions SAR Java/.NET API SQL (JChem Cartridge)

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