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Marvin
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Marvin is a collection of Java tools for drawing, displaying and
characterizing chemical structures, substructures and reactions. Request
Information
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Marvin Applets
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Tools for building
chemical web pages, which are compatible with most browsers
(Internet Explorer, Netscape, Mozilla, Opera, etc.) and have two
GUIs: AWT and Swing. They offer access from/to JavaScript and are
customizable by applet parameters. |
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Marvin Beans
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A set of classes for
building applications. It provides an API with low and high level
classes, and JavaBeans. Marvin Beans support copy and paste
to/from several other structure handling software, import/export
various formats (SMILES, Molfile, SDfile, etc.), and can generate
images (PNG, JPG, SVG, etc.) |
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MarvinSketch/MarvinView
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Applications for end
users which are built from Marvin Beans. MarvinSketch is a tool
for drawing molecules/reactions. MarvinView displays a set of
structures. |
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Calculator Plugins
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Calculator Plugins are an open technology, custom chemical calculation
platform for Marvin and other JChem tools. To try out our plugins please
visit our unlimited predictions implementation. Request
Information
Currently available tools include:
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- pKa
- logP, logD
- polar surface area (PSA)
- charge distribution
- polarizability prediction
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- H-bond aceptor/donor
- major microspecies
- reactivity
- refractivity
- elemental analysis
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JChem Base
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JChem Base is a Java tool for the development of applications that allow
for the search of mixed structural and non-structural data.
JChem Base can also integrate a variety of database systems (Oracle, MS
SQL Server, DB2, Access, etc) with web interfaces and offers fast
substructure, similarity, and exact search engine using 2D hashed
fingerprints. Structures are stored in database tables. Structural and
non-structural data can be combined. SDF, SMILES, etc. can be imported and
exported. The system includes Marvin, a Java based chemical editor and
viewer. Request Information
- Graph based topology search algorithm
- Fingerprint-based database search accelerator technology
- Pharmacophore fingerprint search technology
- Advanced query features;
- exact structure and substructure matching
- generic query atoms
- SMARTS query property support
- R-group query expressions
- reaction queries
- stereo specific structure and reaction specifications
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JChem Cartridge
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Using the JChem Cartridge for Oracle the user can access many JChem
functions, such as structure searching or property predictions, are
available from within Oracle's SQL. Request
Information
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Standardizer
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Standardizer is a structure canonization tool in JChem for converting
molecules from different sources into standard representational forms. Request
Information
Standardizer can automate the identification of mesomers and tautomers and
can be used for counter-ion removal.
- Flexible Molecule Transformation Engine;
- hydrogen manipulations
- aromatic bond transformations
- mesomers
- tautomers
- counter ion removal
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Screen
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Screen is a comprehensive HTS suite in JChem, which works with files and
structure databases and features various models for the similarity
analysis of molecules and pharmacophore hypotheses. Request
Information
The pharmacophore mapping tool offers customizable pharmacophore models as
well as an optimizer to find the "best" screening metrics and
parameter sets.
- Pharmacophore Analysis;
- customizable pharmacophore definition framework (fragment- and
calculation-based solutions)
- integration of plugins
- supporting Chemical Terms
- Configurable Molecule Descriptor Generation;
- chemical topology fingerprints
- pharmacophore topology fingerprints
- hypothesis calculation
- fuzzy smoothing
- Virtual Screening;
- dissimilarity metrics (Euclidean, Tanimoto)
- variable metric modifiers (normalization, scaling, weighting,
directing)
- enrichment enhancement by selectivity optimizer
- screening performance statistics
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JKlustor
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JKlustor is a tool of JChem for clustering, diversity calculations, and
library comparisons based on molecular fingerprints and other
descriptors. Request Information
JKlustor is useful in combinatorial chemistry, drug design, or other areas
where a large number of compounds need to be analyzed.
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Reactor
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Reactor is the virtual reaction engine of Chemaxon's JChem technology.
It supports "smart" reactions (generic reaction equations
combined with reaction rules) generating chemically feasible products even
in batch mode. The professional version of the tool includes support for
multi-step virtual synthesis and filtering of chemically feasible
molecules which are not of interest. Request
Information
Key features:
- chemo-, regio- and stereoselectivity
- main product detection
- intramolecular reactions
- generates an entire synthesis tree at once
- advanced compound dispatching (complex synthesis graphs, trash)
- database, file and memory operation modes
- synthesis rules for each synthetic step (for on-the-fly filtering of
intermediers)
- graphical user interface for browsing the synthesis database
- colored visualization of the original building blocks in the
generated library
- wide range of file formats supported (MOL, RXN, RDF, SMILES, SMARTS,
SMIRKS)
- rapid operation
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Fragmenter
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JChem's Fragmenter uses the RECAP method to create building blocks by
fragmenting larger molecules. Request Information
Fragmenter is particularly relevant for generating analogues of
biologically active compounds for lead discovery.
- Customizable fragmentation rules
- Built-in RECAP fragmentation module
- Fragmentation information is stored with fragments
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