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Focussed and Targeted Library Design
MolMo Services designs focussed and targeted libraries. These are
available both virtual or ready synthesized through one of our partner
laboratories.
The targeted libraries are designed using our SEAL method for specific
templates or lead compounds, or with our High-througput docking
technology. We employ multi-objective optimizations to ensure that the
design are simultaneously focussed, for instance around a synthesis step,
a range of desired ADME properties, or any other desired feature. An example
one-step synthesis library
is shown here.
The MolMo proprietary SYNOPSIS
application generates novel molecules from a
(user selectable) digital catalog of available chemicals and by means of
the extensive synthesis expertise system.
An important feature of SYNOPSIS is that by its nature only synthetically
accessible compounds are evaluated for the library.
The optimization of the designed libraries occurs through the evolutionary competition with previous reaction products generated during a SYNOPSIS run.
High Throughput Screening (HTS)
When large (virtual) libraries need to be reduced to a relevant and
tractable subset, MolMo offers In Silico
screening services either on-site with our
specialized software
or at our own
computing facilities.
The MolMo API provides functionality for In Silico
screening on ADME properties,
Docking,
3D similarity,
etc.
The functionality is available in the form of SOAP procedures, as
web-based cgi modules, or as stand-alone software. The list below shows
the available ADME-oriented functions in the MolMo API. Contact us here for our
HT screening services.
If a required property isn't shown in the table do not hesitate to contact us for a
quotation or more information on
implementing your desired module.
| Property | Input type | Method |
| Molecular Weight | 1/2/3D | atom |
| # Heavy atoms | 1/2/3D | atom |
| # Hbond Donors | 1/2/3D | connectivity |
| # Hbond Acceptors | 1/2/3D | connectivity |
| cLogP | 1/2/3D | connectivity |
| # Rotable bonds | 1/2/3D | connectivity |
| pKa | 1/2/3D | connectivity |
| MolMo fingerprint1 | 1/2/3D | connectivity |
| SASA2 | 3D | (ligand) structure |
| PSA2 | 3D | (ligand) structure |
| logS | 3D | (ligand) structure |
| CACO-23 | 3D | (ligand) structure |
| CYP 3A4 metaboliz. | 3D | (ligand) structure |
| CYP 2D6 metaboliz. | 3D | (target) structure |
| CYP 51 metaboliz. | 3D | (target) structure |
1 The MolMo fingerprint contains 1600 bits encoding for many atom based and topological properties.
The MolMo API supports many distance metrics for similarity and substructure searching on this fingerprint.
2 SaSA and PSA models can be used in a fast gaussian approximation mode.
3 CaCo-2 models exist as PLS-based quantitative prediction, and as a dsicriminatory neural net
for rapid permeable-impermeable assessment of large datasets.
Full 3D structure based screening
MolMo Services also offers target-specific procedures for HTS screening: Compounds can be selected by means of of a relevant low energy pharmacophore (ANTCONF), Steric and Electronic similarity (SEAL) to a target, multiple conformer rigid (SADOCK), or flexible docking (FLEXPHARDOCK) of compound libraries on many systems (See table below)
De Novo Compound Libraries
Based on the 3D-structure of a target MolMo can generate focussed compound libraries that combine high affinity and synthetic accessibility. We have off-the-shelf models available for de novo design or HTS screening for many biological targets. You can request a quotation if you are interested in obtaining a library of compounds for on of the targets below. If the target of interest to you is not shown in the list below, please do not hesitate to contact us for a quotation for the generation of a dedicated model.