[Molvis-list] JChem and Marvin 5.4 launched - 64 bit, multi-threading, enhanced transformations, R-group ordering, new predictor plugin, ECFP, expanded reaction library, disconnected MCS

Alex Allardyce aa at chemaxon.com
Tue Dec 7 10:54:54 EST 2010

Please excuse cross postings

We are pleased to announce the launch of Marvin and JChem 5.4. The major 
new features are listed below along with links to download. JChem for 
Excel and Instant JChem will be released in the next weeks.

Marvin & JChem are software suites of application programming 
interfaces  (API's) and graphic user interfaces (GUI's) used to build 
chemically aware,  platform independent and web ready enterprise 
informatics systems.
Marvin includes structure and reaction editing, visualization and 
structure based property prediction; JChem includes structure management 
and search, library enumeration and library profiling.

Marvin major changes and features
* Full 64 bit support
* Multiple, ordered R-group attachment points - Up to 9 attachment 
points, the order of the attachment points can be  easily changed, and 
the display follows the IUPAC recommendations.
* Enhanced 3D transformations - Rotation around specified axes, 3D 
Plane, mirror, inversion, directed merge of fragments, displaying of 
degree of rotation.
* Context based attached data editing - Attach data to bonds, atoms, 
fragments etc.
* Search for the structure on the canvas as substructure in PubChem 
directly from MarvinSketch.
* Configurable clipboard handling - Control of file formats available 
for copy & paste.
* Fused output option in Markush enumerator - First 100 of enumerated 
structures are shown as a single fused molecule.
* A new command line tool is available for batch mode checking - New 
structure checkers introduced: Empty Structure, Metallocene, Covalent 
Counterion, Ring Strain Error, etc.
* New GUI for training of calculator plugins - Train and run your own 
molecular property prediction with Predictor plugin.
* Industry standard MMFF94 forcefield options - In Conformer Generator 
and 3D Molecular Properties.

Marvin download [http://www.chemaxon.com/download/marvin/]
Release notes [http://www.chemaxon.com/marvin/release-notes.html]
History of changes (all features and bugfixes) 
JChem major changes and features

JChem Base (database management and chemical search)
* Full 64 bit support
* New similarity search result highlighting using Maximum Common Edge 
Substructure (MCES).
* New stereo search options: enantiomer and improved double bond stereo 
* Similarity search is now multi-threaded and results are returned faster
* Fingerprint screening and ABAS are now running in parallel to return 
first results faster.
* More flexible tautomer search - non-tautomer search can consider 
tautomer duplicate tables
* Tables with same name in different databases are supported in 
structure cache
Markush search: New homology groups and properties for Thomson Reuters' 
MMS (Merged Markush Service) database
JChem Web Services: All JChem Manager functionality available
Structure Checker (structure file checking and automated fixing): 
Command line tool 'structurecheck' and new checkers introduced.
Reactor: New virtual reaction library containing systematically listed 
and designed synthetic reactions. 
Standardizer: Built in mesomer and solvent removal transforms
Screen - (Fast/robust 2D and now 3D ligand-based virtual screening)
* extended connectivity fingerprint (ECFP) now available (includes FCFP)
* available both as hashed binary fingerprint and as a list of integer 
JKlustor (MCS and other clustering methods)
* New Maximum Common Edge Substructure algorithm;
  + faster and more robust than previous MCS implementation
  + capable of finding disconnected common substructures
  + pair-wise matching of two sets of structures

JChem download [http://www.chemaxon.com/download/jchem/]
Release notes [http://www.chemaxon.com/jchem/release-notes.html]
History of changes [http://www.chemaxon.com/jchem/changes.html](all 
features and bugfixes)

Registered forum users can automatically generate 2 week evaluation 
licenses for all products: http://www.chemaxon.com/my-chemaxon/
Non commercial academic users can obtain free licenses for all products, 
information and application form: 
*Alex Allardyce*
Marketing Dir.
Maramaros koz 3/A, Budapest, 1037 Hungary
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa at chemaxon.com

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