CAChe Research Computer-Aided Chemistry & Biochemistry
EMPIRE
Chemical and physical property prediction from electronic properties of molecular surfaces
by
A caddle® is a customizable and entirely web-based molecular modeling system developed jointly by Cepos InSilico and Molcad GmbH that offers high-quality interactive 3D-visualization combined with advanced flexible workflows and protocols for modeling tasks. caddles may have specific functions (such as the logP-caddle), or may function as general, user-configurable web-based modeling systems. The unique feature of caddles is their proprietary 3D visualization technology that allows a caddle to be used on any suitable device (desktop, laptop, tablet, mobile phone) equipped with a suitable web browser.
SAR-caddle® is a customizable web-based tool for building & applying robust QSAR/QSPR models with applicability domain analysis & 3D visualization. It features Shepard interpolation, PLS and an extremely robust bagged stepping linear regression designed to eliminate descriptor bias for datasets with very many descriptors. SAR-caddle requires only a suitable browser on a desktop computer, laptop, tablet or smart phone (no local installation required).
EMPIRE™ is a completely new semiempirical molecular
orbital program designed to run in parallel on multi-core
desktop computers and on massively parallel supercomputers. EMPIRE can currently perform calculations using s-, p-
and d-orbitals in the basis set with the core-core functions
from MNDO, MNDO/d (also PM6 and AM1*), and AM1
(also AM1*, PM3, PM6). The largest calculation performed
to date ran efficiently for 76,800 atoms on 1,024 processors.
ParaSurf™ uses semiempirical methods to calculate electronic properties on the surface of molecules for use in QSPR, 3D-QSAR, ligand docking and reactivity prediction, such as Cytochrome P-450 drug metabolism. ParaSurf™ is the basis module that uses output from a semiempirical molecular orbital program such as Cepos Mopac 6 or VAMP to construct molecular surfaces and calculate local properties and descriptors. Surfaces may be generated by shrink-wrap or marching-cube algorithms and the former may be fitted to a spherical harmonic series. ParaSurf™ from Cepos InSilico was originally introduced in 2005.
ParaSurf™ can also generate local enthalpies and free energies of solvation and integrate them over the entire molecular surface. The application has the ability to read Surface-Integral Model (SIM) files that allow it to calculate properties such as the enthalpy and free energy of hydration plus the free energies of solvation in n-octanol and chloroform.
The methodologies for predicting Cytochrome P450 drug metabolism (CypScore) and for improved ligand docking accuracies, are described in the links below.
FREE Academic version of ParaSurf
A special academic version of ParaSurf which includes most of the functionality of the commercial release, is now available at no cost to bona fide academics. Click here to get your copy...
Cepos Mopac 6 is a modified version of the public-domain Mopac 6 (QCPE 455) that writes the files necessary to run ParaSurf™. Cepos Mopac 6 serves as a freeware alternative to commercial semiempirical molecular orbital packages for ParaSurf™ users. The program is adequate for MNDO, AM1 and PM3 calculations. However, it does not include many modern options and Hamiltonians (in particular, it does not include methods that use d-orbitals). We recommend that the EF geometry optimizer always be used as the default. BFGS optimizer often exits at high values of the gradient norm.
Cepos InSilico was created to make the science developed in the Parashift Project readily available and to support further research and development. (The Parashift Project, was born at the 2002 EuroQSAR conference at Bournemouth in the UK as a concerted attempt to break out of the mould of conventional atomistic modelling techniques with methods based on local molecular surface properties.) As a result, Cepos InSilico's surface-based modelling techniques provide in silico screening, modelling and simulation software designed to give accurate, generally applicable predictions of biological activity, reactivity, ecological impact, ADME and physical properties.
Researchers from the universities of Erlangen in Germany, Portsmouth in the UK and LORIA (Nancy, France) work together developing products marketed by Cepos InSilico Limited. The areas of expertise of the three research groups range from classical simulation and quantum mechanical techniques to analytical representations of irregular bodies and interpolation techniques for QSAR and QSPR. This expertise provides the uniquely powerful scientific background behind today's Cepos technology.
Annual lease price $USD per floating license token
Cepos products are available for annual lease for Windows and Linux, in both 32-bit and 64-bit
versions. Only commercial and Government licenses include full support and updates. Cepos
applications such as ParaSurf™ use a token licensing system. One application per token may run at
any one time. CeposLM™ is installed on a central license server that must be available to all licensed
users, (this may be your PC hardrive if you have only a single-user license). ParaSurf pricing is as
shown below, MOPAC6 is free.
SUPPORT
Industrial and Government licenses include full Email and telephone support, maintenance and annual updates. However, Academic licenses do not include support or updates.
CEPOS Email Support: support@ceposinsilico.com
CEPOS Telephone Support (Germany): 011 49 9131 970 4446 (from USA)
CEPOS Fax: 011 49 9131 970 4911 note that Germany is 6 hours ahead of Eastern Standard Time (NY, USA)
• Cytochrome P450 drug metabolism prediction* • Ligand docking - improved accuracy** • 3D QSAR & QSPR - novel electronic descriptors • Chemical & physical property prediction...
