AKos GmbH Newsletter January 2011
AKos Consulting
& Solutions Deutschland GmbH
Telephone
+49 7627 970068
Fax
+49 7627 970067
Fax to Mail
+49 1805 744743 8318
E-Mail
General
Information:
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Confirm or reject future newsletters Our mailing list is generated mainly from business correspondence. We use automatic procedures to do this. Please send an email to subscribe@akosgmbh.de if you want to receive future newsletter, or send an email to unsubscribe@akosgmbh.de if you want to be removed from the mailing list. Please forward this to a friend, who might be interested. |
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CWM Global Search allows searching the Internet by structure, synonym and CAS Registry Number. In a Quick Search, we return structure, names and CAS Registry Numbers* within seconds. The Global Search allows a comprehensive search and the resulting links are organized by topics. A search by name can automatically invoke another search by structure and/or CAS Registry Number, or any combination of these. CWM Global Search presently searches 50 free chemical and pharma relevant databases -- containing more than 100 million pages which associate chemical structures with data. All you have to do is to open the URL http://cwmglobalsearch.com/gsweb in your Internet Explorer or Firefox on Windows, or Safari on Macintosh. --> |
We are selling the CWM Global Search web service. What is this, and for
what would this be good? What is it? We generate for the structure up to 6 identifiers, 2 InChI keys, 2 InChI names, molfile and smiles depending on the resources selected. We send this information and the free text queries to now more than 50 resources on the web. This web service could be configured from us and installed at a customer site. We also would deliver updates if new resources are added. The results are a collection of links. What can you do with this?
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At the first time you
will be asked to install the Microsoft Silverlight Plug-In, provided it
is not already installed. We recommend to start by reading the installation notes at cwmglobalsearch.com/installation. A free version is available that is restricted to searches at Google, PubChem, ChemSpider and AKosSamples. The full version is 240 Euro per user. We sincerely are interested in your feed-back. Please use the feedback button in the application. |
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Some of the new sources in CWM Global Search | ||||||||||||||||||
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Spot the difference -
and get it right! |
Proteax®
for Spreadsheets 1.3 released
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Proteax Desktop and Proteax Cartridge downloads With the release of Proteax 1.3 all Proteax products will be available for direct download from the Biochemfusion web site.
Discounted licenses until year-end |
Can your chemists and
bioinformatics people agree ? Is it a structure ? Is it a sequence ?... Imagine that they used Proteax - a consistent way of representing biopharmaceuticals that lets you see molecules as sequences or structures as you please. "Can you generate 1000 controlled mutations for me this afternoon ?" Applied DerNot expressions let you create protein derivatives through simple Excel expressions. With chemically consistent results. |
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You only know what you have experienced! Our co-workers have a lot of experience.
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AKos GmbH works with Evolvus System that offers as service to build custom made databases for chemical and pharmaceutical companies. This can be databases for a few compounds with all available data, or databases for many compounds with customer selected fields. This can be excerpts from patents or a subsets of already collected data to 3.8 million compounds. | |||||||||||||||||||
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Predict biological activities with data you can trust
Support the decision-making process and accelerate discovery Predict biological activities and assess off-target risks Repurpose drugs through new indications Optimize lead identification through in silico screening |
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AurPASS® (Aureus Prediction of Activity Spectra of Substances) is a software tool which exploits high quality experimental SAR data to generate in silico biological activity profiles of new substances. AurPASS® is a ready-to-use software tool running with several SAR bases extracted from the Aureus knowledge bases. These include GPCR, Kinase, Ion Channel, Nuclear Receptor, Protease, and hERG. AurPASS® is the result of the combination of first-in-class systems and high level expertise provides robust computer-assisted estimates with more than 90% accuracy. |
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What's new for PASS?
PASS (Prediction of Activity Spectra of Substances) predicts Biological Activity Spectra of compounds. The Biological Activity Spectrum (see right column) of a compound is the collection of pharmacological effects, physiological and biochemical mechanisms of action, specific toxicities (mutagenicity, carcinogenicity, teratogenicity, embryotoxicity, etc.) that can be revealed in a compound's interaction with biological systems. The Biological Activity Spectrum describes the intrinsic properties of the compound dependant on its chemical structure.
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Are you familiar with workflow programs? Wouldn’t it
be a good idea to have a program that reads a file or gets information
from a database, filters the structures by certain criteria, predicts
PASS parameters, compares these parameters with known experimental
results, selects structures by more criteria, does some modeling, i.e.
docking and all you have to do is punch a button? KNIME and Pipeline Pilot are for chemists the best workflow solutions (in my opinion). KNIME is free, and support is offered by the KNIME company. Pipeline Pilot is sold by Accelrys and has many more nodes and functionalities. 1. Vladimir Poroikov’s group is working on a KNIME node. If required, we can develop a Pipeline Pilot node. 2. Since my programmer is a .NET specialist we developed on Microsoft’s Workflow Foundation a workflow CWM Lead Finder. CWM Lead Finder finds biological similar compounds in two different SDFiles that you can sort by structure similarity, PASS accuracy, and toxicity parameters. 3. The company Aureus collects structures, quantitative and qualitative test data. The idea is to build a comprehensive biological profile of compounds using experimental and predicted data, see above. They have built databases in these areas: It is expected that the profiles will have many missing data. Aureus has developed knowledge bases i.e. AurPASS GPCR Predictor that augment the experimental data. Now, you can see exactly which compounds were used to build the knowledge base in PASS. |
Biological Activity Spectrum of a
compound. Pa = probability that the compound has
this activity Only a few of the more than 4000 activities are shown for which PASS is trained.
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Drug Data Report |
Drug Data report is one of the most used databases to get structures and biological effects. MDDR is very handy to get SDFiles with compounds of desired activities. We managed to load the MDDR SDFile into Isentris Personal Edition. Isentris Personal Edition is the successor of ISIS/Base. This means you have now a solution to work with MDDR without the need to install a server system. Isentris Personal Edition is strictly a personal system. You cannot install it on a server. MDDR is licensed by Accelrys. | |||||||||||||||||||
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WEBINARS
Product:
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Thursday 13th of January 1:30 PM UK Time Title: An Introduction to Discovery Studio 3.0 – Tien Luu / A. Stevens Abstract: The release of Accelrys’ Discovery Studio 3.0 in November extends our portfolio of small molecule drug design and market leading biological simulation tools and is focused on bringing new science from Accelrys and our partners, improved performance, and key enhancements to our users. This webinar will introduce users to key enhancements within the client designed to improve usability and encourage collaboration, as well as providing an overview of the new scientific developments. Thursday 10th of February 1:30 PM UK Time Title: Protein Design tools in Discovery Studio 3.0: Computational stability prediction and Computational Alanine Scanning – Anne Goupil / A. Stevens Abstract: One of the primary goals of protein design is to engineer optimized proteins by introducing mutations. Protein thermal stability is a key issue for chemical, biotechnology and pharmaceutical industries. We will present a new set of tools available in Discovery Studio 3.0 and show how to calculate mutation energies as well as predict stabilizing mutations Similarly, Protein-protein interactions are a key components of signal transduction.. Methods for predicting energetically important amino acids (interaction hot spots) at protein-protein interfaces are of increasing interest. We will present a new set of tools available in Discovery Studio 3.0 and show how to predict computationally derived interaction hot spots. Computational results will be compared to experimental data on a set of selected examples. Thursday 24th of February 1:30 PM UK Time Title: Automatic Creation and Validation of Pharmacophores derived from Receptor-Ligand Complexes Tien Luu / A. Stevens Abstract: A pharmacophore is a model which represents the key physico-chemical interactions, between a receptor target and ligand, that mediate biological activity. In DS 3.0 users can automatically create a series of pharmacophore models representing a receptor-ligand complex, and have these validated with known active and inactive compounds to determine the best pharmacophore for hit/lead identification. Thursday 10th of March 1:30 PM UK Time Title: Discovery Studio 3.00 /Pipeline Pilot 8.00 Integration - Anne Goupil / A. Stevens Abstract: Discovery Studio is build on Pipeline Pilot™ platform technology, it is therefore possible for scientists to access any computational codes available in Discovery Studio at the Pipeline Pilot level. We will show through examples how scientists can customize or build their own protocols to automate tasks and or meet their precise needs. |
AKos GmbH is the exclusive reseller for Accelrys in the countries East of Austria until the Chinese border and South until Turkey, with the exception of academia in Russia and Poland. The products of Accelrys are:
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* CAS Registry Number® and Synonym CAS Registry Number, SciFinder are registered trademarks of the American Chemical Society (ACS). All Rights Reserved. JDraw is a Java applet structure editor from Accelrys, Inc.
