Molegro has released a new version of Molegro Virtual Docker, an
integrated platform for predicting protein-ligand interactions.
Molegro Virtual Docker enables chemists to computationally predict and
visualize how small molecules interact with a protein receptor, making
it possible to understand and rationally optimize potential drug
candidates. Even if the 3D protein structure is not known, it is still
possible to make predictions based on similarity to known binders, or
to train regression models based on molecular descriptors - all inside
an integrated graphical environment.

In Molegro Virtual Docker 5, it is now possible to take advantage of
Graphics Processing Units (GPU’s) to greatly accelerate the docking
simulations. Though GPU’s were originally designed for pure
visualization purposes, their computational power has now outpaced
traditional CPU’s, making them an attractive target for demanding
scientific computations. Using the GPU acceleration in Molegro Virtual
Docker, it is now possible to predict how a molecule will bind to a
target receptor in less than one second on a single machine - making
it more than twenty times faster than a pure CPU-based approach.

ahsystems group provides a global team of experienced and quality consultants and developers with the latest industry knowledge needed to deliver business and technical consulting projects and staffing solutions.

Technical Solutions

Our technology team creates solid and scalable solutions that bring quality value to your entire organization. We have extensive expertise in .Net, C#, JAVA, PHP, MySQL, and many other languages, databases, and platforms and specialize in:

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• Open source web applications and development

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• Construction Quality Management
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• Cost Estimates
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• Claim Evaluations

Molegro Virtual Docker is an integrated platform for predicting protein - ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.

Molegro is pleased to announce the release of Molegro KNIME Extensions. New versions of Molegro Virtual Docker (MVD), Molegro Molecular Viewer (MMV), and Molegro Data Modeller (MDM) have been released, all with support for KNIME (see link below for release notes).

KNIME Extensions Repository

* Support for custom coloring of molecules (atoms, residues, rings).

* Visualization of hydrogen bonds and electrostatic interactions can now be customized.

* Visualization settings (e.g. graphic styles, camera settings, custom

coloring) is now stored in the workspace file (MVDML).

* PDB header information and SDF annotations is now imported and stored as part of the workspace.

* Improved parsing of PDB files (e.g. using PDB Compliancy information if available and refined thresholds for detecting covalent bonds).

* Minor user interface improvements and bug fixes.

Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity.

Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity.

The Molegro Virtual Docker (MVD) has been shown to yield higher docking accuracy than other state-of-the-art docking products (MVD: 87%, Glide: 82%, Surflex: 75%, FlexX: 58%).

The Molegro Virtual Docker (MVD) has been shown to yield higher docking accuracy than other state-of-the-art docking products (MVD: 87%, Glide: 82%, Surflex: 75%, FlexX: 58%).

Molegro Virtual DockerVersion (Academic/Gov or Commercial):

Commercial $11,429—Please contact us to order

We have updated our list of journal papers documenting the use of Molegro Virtual Docker in various contexts.

The new updated list is available on our website: http://www.molegro.com/mvd-technology.php

HyperChem 8 Pro now available.

SALE:  HyperChem Pro 7.5 $649

HyperChem Pro 8.x $829 edu/govn’t

(limited time only)

For detailed info on Hyperchem.

HyperChem 8.0.6 is only a minor improvement over 8.0.5, this release fixes a bug in particle-in-box calculations and problems in sometimes displaying aromatic bonds.  The previous update, Release 8.0.5, featured mainly graphics improvements over 8.0.4. You can download the free update directly from Hypercube, the developers of HyperChem (registration required). ahsystems group is an authorized reseller of HyperChem. You can read more about HyperChem — a sophisticated molocular modeling environment that is known for its quality, flexibility, and ease of use — and purchase the software here on our site.

Our partner Molegro is pleased to announce a new release of Molegro Data Modeller, a cross-platform application for data mining, data modelling, and data visualization.

Molegro Data Modeller offers a high-quality modelling tool based on state-of-the-art data mining techniques combined with a user interface experience focusing on usability and productivity.

The highly interactive user interface of Molegro Data Modeller is ideal for fast and intuitive data exploration, as opposed to complex workflow based solutions or command-driven statistical products. Molegro Data Modeller is available for Windows, Linux, and Mac OS X.

New features in version 2.5:

• Classification models. MDM now supports the following multi-class classification models: K-Nearest Neighbor and Support Vector Machines with Linear, Radial, Sigmoid, and Polynomial kernel functions. The classification models support automatic optimization of model parameters and feature selection.
• Chemistry module. MDM is now able to show 2D depictions of molecules. Molecules may be imported in SDF format or as SMILES strings. Molecules may be depicted inside the spreadsheet cells or in a separate grid window. It is also possible to visualize the molecules directly in the 2D plotter and optionally cluster overlapping molecules.
• A new Bivariate Analysis dialog for analyzing classification results (confusion matrix, precision / recall, F-measure, and several other measures).
• A new threshold-based clustering method.
• Minor user interface improvements and bug fixes (see Release Notes for details).

About Molegro

Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience.

Green IT. Sound too good to be true?

You may be listening to the incessant hum of fans and air conditioners in your data warehouse and be thinking “is their a way to save money here and help the planet while we’re at it?” You (and your organization) are not alone. According to Business Week:

Major public steps by major corporations—surely in part marketing moves to seem committed to taking action in terms of ‘green’ practices and policies—align with some of the key points in three recent reports, published by leading research and management consulting firms Forrester Research, Gartner, and McKinsey. [See also The Real Costs of Saving the Planet, (BusinessWeek.com, 12/4/07).]

The reports highlight the costs and savings possible from implementing green strategies— and ultimately reducing greenhouse gas emissions. Containing a blend of ideas, warnings, and analyses, the reports are aimed at technology companies (and, in the case of the McKinsey report, governmental, private, and other groups) looking to develop more environmentally friendly policies—both within their own organizations and for their customers.

Are you ready to develop a green IT policy? Looking to put your old, energy-hungry server farm out to pasture? Contact us and let us help you make the transition. Do it to help your bottom line… and the Earth beneath your feet.

Molcode to bring toolboxes, Databases and Reach Service

Check out the new On-Line Demo of Molecode Toolbox

MolCode, Ltd. is a dynamic company developing unique in silico technologies for the computational prediction of the properties of chemical compounds and materials and for the prediction of the molecular structure of compounds and materials with predetermined properties.

Molcode provides services and contract research on the computational prediction of the properties of chemical compounds and on in silico molecular design including hit identification, hit-to lead development, and lead optimization. Our technologies have been successfully used for the identification of drug candidates against CNS diseases and antivirals.

Molcode Toolboxes are unique software for the prediction of a wide range of experimentally unknown values of properties of compounds  including physicochemical, biological, ADME-Tox, ecological pathways/ecotoxicity and adverse drug  effects.

Molcode Database holds around 300,000 optimized (semi-empirical, ab initio) structures, their respective descriptors and property values.

Reach Service:

Introduction

One of the most significant new European initiatives is the European Chemicals Registration (REACH) program. Molcode is taking part in this program and can offer data on endpoints such as acute toxicity, mutagenicity, carcinogenicity, eye irritation etc. for a large number of compounds covered by REACH.

Molcode Database covers most of the chemical, physical, biological, biomedical endpoints which are allowed or even suggested by REACH to be modeled with QSAR methods in order to avoid expensive laboratory tests and animal tests.

Molcode is a data holder for a wide range of organic compounds. All the predictive models and their respective predictions for a single endpoint for a single compound are statistically validated and an applicability domain test is performed for each single model/compound.

The endpoint data for a single compound is provided in QSAR Property Report Format (QPRF).

Sample endpoints:

Activated sludge toxicity (EC50)
Acute toxicity   B.1 tris/ bis
Acute oral toxicity (LD50)
In vitro cytotoxicity (IC50)
Chronic toxicity LOAEL (rat) B.30
Eye Irritation (MMAS/P) B.5
Carcinogenicity: rat, mouse (TD50, various sets) B.32
Mutagenicity (salmonella TA98, TA100, various sets) B.13/14
Acute toxicity to fish (lethality) C.1
danio rerio
fathead minnow
rainbow throut
Bioconcentration factor for fish #1 (BCF, various sets) C.13
Microbial inhibition (activated sludge respiration inhibition) C.11
Endocrine Activity: Estrogen receptor-binding
Gastrointestinal absorption
Permeability Caco-2 monolayer
Permeability PAMPA (logPapp (pH5,5)) MMFFS
Permeability PAMPA (logPapp (pH7,4)) MMFFS
Blood-brain barrier penetration
Skin irritation/corrosion  B.4
Skin sensitisation B.40
Organic carbon-sorption partition coefficient (organic carbon; Koc) C.19
Short-term toxicity to Daphnia (immobilisation, LC50 96h) C.2
Toxicity to honey bee C.17
Toxicity to tetrahymena pyroformis (IGC50)

For more detailed information and available endpoint data for your compound/product please contact: info@ahsystem.com.

Downloads:
Sample QMRF for „Eye Irritation“ accepted by JRC
Sample QPRF for formaldehyde (ready for dossier submission to IUCLID5)