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

news · 11 years ago

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 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 ~ 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 options
  • 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 supported
Structure Checker (structure file checking and automatic fixing)
  • Command line tool structurecheck and new checkers introduced.
Reactor - 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 features
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 ~ History of changes (all features and bugfixes)