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Custom Software
Because of our versatile API and the high level of pharmaceutical and
chemical expertise of our programmers MolMo Services has developed and
implemented novel computational methods dedicated
We can provide applications for computer systems ranging from a desktop
system to the largest clusters. MolMo Services is constantly active in
the development of new algorithms and the implementation of
computational chemistry technology for our customers.
We also provide customized solutions and scripting to automate
your molecular modeling work-flows and SOP's for drug design and
in silico screening both as
These dedicated work-flows make use of our many off-the-shelf applications
shown below and provide a high level of
consistency and automation in the targeted and focussed library design.
Common bundles of software can be licensed together for specific projects,
for instance: the automatic de novo generation
of close analogs with suitable physicochemistry is implenmeted as a
work-flow using the SYNOPSIS-MOLPROPS-NSGASEAL applications.
Similarly the discovery of new scaffolds by means of docking is done
by a work-flow consisting of our PROSA-SYNOPSIS-GACS-SADOCK modules.
For a quotation
for your drug design challenge please contact us here.
Off-the-Shelf Software
SYNOPSIS is a de novo drug design application that includes a synthesis route for each generated molecule. SYNOPSIS designs novel molecules by starting from a database of available molecules and simulating organic synthesis steps. This way of generating molecules imposes synthetic accessibility on the molecules. Click here or a more detailed description of SYNOPSIS. For information about SYNOPSIS software licensing please contact us here.
GACS is a genetic algorithm based program for conformational search of flexible molecules. For small molecules GACS consistently generates all low energy conformers. The conformers are fully relaxed using molecular mechanics. For information about GACS software licensing please contact us here.
SADOCK is a simulated annealing algorithm for rigid docking of the low energy conformers of a putative ligand into the binding site of a target enzyme. It uses pre-calculated grids for fast evaluation of the ligand-target interaction. For information about SADOCK software licensing please contact us here.
ANTCONF is a ant algorithm that searches the torsional degrees of freedom of a flexible molecule to determine the molecular mechanics energy of the lowest energy conformer. The details of the ANTCONF algorithm A reprint of the paper on the algorithm can be found here. ANTCONF can be used to rapidly generate superior 3D geometries that allow for high qualitity pharmacophore searching. For information about software licensing please contact us here.
FLEXPHARDOCK is a flexible docking algorithm based upon a pharmacophore model of a target enzyme. FLEXPHARDOCK is primarily intended for highly flexible molecules where the generation and docking of all low energy conformers is unpractical. For information about FLEXPHARDOCK software licensing please contact us here.
NSGASEAL Is a program that can be used to design chemically diverse, but functionally analog compounds. NSGASEAL sumperimposes flexible molecules on a rigid target structure by means of a bifunctional minimization algorithm which simultaneously maximizes the steric and electronic (SEAL) overlap and minimizes the internal conformational strain of the compound. The result is a set of analog compounds of the target that constitute the pareto optimal solutions of the search space. The details and an example of an application of the NGSASEAL algorithm can be found here, a live demo of the NSGASEAL method embedded in a cgi-application is available here. For information about NSGASEAL software licensing please contact us here.
PROSA Is a tool to automatically generate optimal hydrogen bond networks in X-ray structures. With PROSA the end groups of polar residues and water molecules are optimized by means of a simulated annealing approach (in rotational space), thus allowing for much more reliable docking of compounds in X-ray structures. More details and a sample of a PROSA-generated structure can be seen here. For information about PROSA software licensing please contact us here.
Q is our visualization tool. Q is designed to render and manipulate molecular data files at high speed even on standard hardware. Q will effortlessly load, render and modify thousands of small molecules simultaneously on a typical laptop computer (see for instance this screenshot of Q). Furthermore Q has a built-in cross-site collaboration engine which allows users from may different sites to interact with objects across a secure network connection. Q has a strong scripting engine, and allows for batch mode as well as interactive processing. For information about Q software licensing please contact us here.
MuMo is an non-interactive integrated molecular modelling application that can be run as a background service (on Windows) or daemon (on MacOS X, Linux, Irix, HP-UX, AIX) in a heterogeneous network. The MuMo-client will accept requests from a dedicated server to perform conformation search, docking, geometry optimization, molecular dynamics, etc. during idle cycles of the clients' cpu. MuMo thus instantly provides a hetergeneous massively parallel grid solution for molecular modelling problems. For information about MuMo software licensing please contact us here.
Molprops is an application that computes the physicochemical and 1/2D based properties of arbitrarily large data-sets. It can be used either as part of a web-based (SOAP) workflow, or as stand-alone application. For information about Molprops software licensing please contact us here.
New Software Tools for Drug Design
The continuing commitment of MolMo Services to innovation is clear from the
scientific output: our staff
have published more than 50 papers on medicinal chemistry, computational techniques,
and many other topics. They also appear as inventors on 20 worldwide patents in disease areas ranging from virology through
neurology to oncology.
Examples include Ab initio docking
(abida), an Ant algorithm for
conformational analysis and the pareto
optimal flexible alignment of molecules.
More than software
Support
Our software is developed
by experts in the field and our software developers are also available
to customers with support questions.
Technical communication with our customers is therefore efficient and
effective; questions are dealt with immediately, without long update cycles.
We can also help you integrate our software and models in your grid or
cluster environments.
Software Licensing
MolMo Services follows a grid- and cluster-friendly licensing policy.
When you consider running computational software on more than just a
few nodes you will
find our offering very cost effective.
Computing Center
MolMo Services operates a
computer center for
computational and research services for our customers.
This service is available on
both project- and fee per compound basis. Customers who normally would
not operate the required infrastructure and staff for extensive
computational studies can profit from the expertise and the facilities
of MolMo services. The availability of the computing center also
ensures that the software developed by MolMo Services is
stress-tested in a demanding parallel computing environment
before it is shipped to the customers.