2014-04-15 17:08
New release: FLAP 2.0 & WaterFLAP

We are very proud to announce the release of FLAP 2.0 and WaterFLAP for virtual screening, pharmacophore modelling, 3D-QSAR, docking, and water prediction.

FLAP 2.0 contains a number of significant enhancements compared to FLAP 1.0. WaterFLAP is a new approach based on GRID MIFs to predict site water locations and networks; the waters are then scored using the new CRY field (combined hydrophobicity and lipophilicity), ENTR (to estimate the entropic character), and the OH2 water enthalpy. These scores quickly enable determination of structural, displaceable, and bulk waters, and have been used to predict the kinetics of binding. The docking algorithm FLAPdock has been extensively re-parameterised and validated on hundreds of crystal structures including the Astex and DUD datasets. Additionally, FLAPdock is able to use the WaterFLAP waters to guide pose prediction, giving improved results where bridging waters are critical for binding. The GRID procedure is now accessible from within FLAP to allow full binding site characterisation and analysis.

More information about FLAP can be found here

2014-02-17 12:54
ABSCIEX & Molecular Discovery joint meeting 2014.

We are very pleased to announce the user joint meeting between Molecular Discovery Ltd. and AB SCIEX.

This meeting will show the new features of MetaSite, Mass-MetaSite, WebMetabase from Molecular Discovery as well as Metabolite Pilot WP from ABSCIEX, practical hands on sessions on these software with the experts and presentations from users on how they enhance their workflows by using our software.

The meeting is address to ADME, Metabolite Identification experts and user of Metabolite Pilot/MetaSite-MassMetaSite-WebMetabase users.

The meeting will be held at the Molecular Discovery facilities in Perugia Italy on the 15th and 16th of May 2014.

The number of places are limited. Please, contact us as soon as possible

Ismael Zamora (
Gary Impey (

Meeting Agenda

Download the meeting agenda and the location details here

2014-02-05 13:23
New release of WebMetaBase 2.0 and Mass-MetaSite 3.0

WebMetaBase is a server-based application that is used for metabolite identification data  storage, reviewing metabolite identification experiments, and extracting the maximum knowledge from the information loaded into the system.

We are now pleased to announce the release of version WebMetaBase 2.0 with new and improvement capabilities to further streamline experimental protocols like metabolite identification, reactive metabolite trapping, Soft Spot identification, etc.

New features in WebMetaBase 2.0

  • New search capabilities:
    • Definition of search domains.
    • Save searches ( criteria and result snapshot).
    • New view for the search results in the form of a table (review tool).
  • User control enhancement in the experimental analysis:
    • Experimental flag system, user defined chromatographic filters, re-numbering of metabolites, user defined metabolite names, metabolite group definition, customizable view of the chromatogram data, manual edition for Markush structures, etc.
    • Handling of isotopes.
    • Handling of UV signal and Radio signal in the chromatogram browser.
    • Specific workflows for GSH trapping experiments.
  • New protocol controls:
    • Enable/disable protocol to be used.
    • A specific replicate variable and calibration variable definition.
    • Assign protocol instances directly to a folder.
  • New Analysis tool called Fragment Analysis: to search in approved experiments for specific substructures to study frequency of metabolism and reactions involved.
  • Administrative controls for maintenance and new documentation to develop the IT WebMetaBase infrastructure.

Mass-MetaSite is a new approach for the automatic identification of metabolites from Liquid Chromatography – Mass Spectrometry data, reducing manual analysis from several hours to only a few minutes per compound

We are now pleased to announce the release of version Mass-MetaSite 3.0 with improvements in signal treatment and also with new workflows that helps in the daily work of ADME scientists.


New Features in Mass-MetaSite 3.0

  • Exclusion List for m/z values made available for MS peaks.
  • Improved chromatogram peak correlation measurement for a more accurate filtering of the MS spectrum.
  • Customizable neutral loss and fragment ion definitions for GSH metabolites detection.
  • Added cyanide and methylhydroxylamine trapping.
  • Easy activation/deactivation of uncommon reactions.
  • Improved discarding of metabolites peaks coming from background noise.
  • Importing and exporting of GUI and batch processor settings.
  • Processing of Radio files now supported by the batch processor.
  • Automatic filtering of unusual metabolites for Markush simplification.
  • Typical Glucuronide neutral loss (-176) taken into account for MetId.
  • SD File format exporting.
  • Activation/Deactivation of double-charged peak search. Improved isotopic pattern checking for double-charged ions detection.
  • Better smoothing algorithm for chromatogram peak detection. Smoothing level can now be fine-tuned inside the settings.
  • Batch processor sample list wizard for direct interaction with WebMetaBase 2.0.


2014-01-20 9:16
New Release: MoKa 2.5

We are pleased to announce the release of MoKa 2.5 for fast and accurate pKa, tautomer, logP, logD and IEP modelling.

As with every version, many literature compounds have been experimentally retested to improve our confidence in the models; with this release 40 of the 55 models have been recomputed based on this new data.

Additionally, structural input has been improved to make it more efficient and less affected by external factors; for example, counterions are now automatically stripped during LogP-LogD and IEP calculations.

Recognized ionizable centres that are predicted with lower certainty are now shown, to enable Users to see where they should focus their efforts to improve the provided models.The molecule isoelectric point (IEP) is now computed. Finally, the model training module Kibitzer is now accessible command-line, enabling users to automate custom model building as new company data is obtained.

More information about MoKa can be found here

2013-06-26 14:35
Update: PharmBench 1.0 webservice

PharmBench 1.0 is a community benchmark dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches, containing 960 aligned ligands across 81 targets. The pharmbench.moldiscovery.com site has now been updated with a web service, so that users can score their own alignment models using the same objective scores described in the original publication.

Latest versions




Register | Lost password?

MIF book
book owners access