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|Every chemist and biologist
CWM Global Search - the underlying
|Scientist analyzing and working with Proteins
New version Proteax
1.3 - protein variants made easy
AKos GmbH has
resources for Oracle
programming and for chemoinformatics projects.
|Medicinal chemist, modeler,
AKos GmbH signed an agreement with
Systems for providing the
service to generate custom made databases.
AurPASS® (Aureus Prediction of Activity
Spectra of Substances)
developments in PASS.
MDDR as personal desktop application.
||Webinar schedule for
Discovery Studio from Accelrys
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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
any combination of these. CWM Global Search presently
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
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?
The chemist has an in-house application to search for suppliers. He
has access to SCD, ACD and CHEMCATS. If he cannot find a supplier,
or only Chinese ones, one can offer him a “button” and he sends his
query to the Internet for a complete search. Such a “button” could
be built quite easily in Isentris. One can imagine many applications
where the user wants to augment his in-house searches by a more
complete search, i.e. for patents, biological activities, spectra,
has a node to access web services. The user could send a SDFile to the
CWM Web Service, and where he find hits he can invoke other web
services (there are about 1000 available right now) to display data
and not only links.
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
A free version is
available that is restricted to searches at Google, PubChem, ChemSpider
The full version is
240 Euro per user.
We sincerely are
interested in your feed-back. Please use the feedback button in the
Some of the new sources in CWM Global Search
Spot the difference -
and get it right!
Can you name proteins just by looking at them? Proteax DerNot
expressions clearly show you how much two proteins differ. Works with
cyclic chains too.
Protein SAR tables - impossible you say ? No, not at all.
Proteax can name your biopharmaceutical candidates so you get consistent
and meaningful labels for your protein SAR tables.
Having trouble with your weight ?
Does the analytical department claim a molecule weight of 9243.5 Da but
your sequence says 9202 Da ? Let Proteax enable seamless communication
between mass-spec and medicinal chemistry.
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.
for Spreadsheets 1.3 released
Proteax for Spreadsheets 1.3 is now ready for download. Improved layout
and graphical rendering of chemical structures.
You can get a fully functional trial version of Proteax for Spreadsheets
by downloading it here.
- The image to the right is an actual rendering of Cyclosporin CsA
generated directly from sequence. Unmodified natural amino acids are
shown as green "bubbles".
- Optional name and number residue labels.
- 64-bit Microsoft Excel® 2010 directly supported.
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.
- Proteax Desktop - Use Proteax from .NET, Python, Pascal, or
- Proteax Cartridge - Use Proteax SQL extensions and indexing
inside Oracle® databases.
Discounted licenses until year-end
There is still time to get a Proteax for Spreadsheets license for only €
350,-. This is an introductory offer that expires December 31st.
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.
You only know what you have
experienced! Our co-workers have a lot of experience.
We sell programs and cooperate with
people for building applications. One of us has 18 years Oracle
programming experience. His development tools for ORACLE enable us
to build applications in days instead of months.
Some of us have 20 years experience
building chemoinformatics applications in low and high throughput
screening, and building and merging structure databases.
Others co-workers have
experience training commercial and in-house programs.
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.
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
(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.
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.
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.
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.
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
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
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:
Pharmacology Space (GPS)
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
X-Axis = Pa-Pi
Y-Axis = Activities
Pa = probability that the compound has
Pi = probability that the compounds does not have this activity
Only a few of the more than 4000
activities are shown for which PASS is trained.
Drug Data Report
as desktop application
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.
of January 1:30 PM UK Time
An Introduction to Discovery Studio 3.0 – Tien Luu / A. Stevens
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
Protein Design tools in Discovery Studio 3.0: Computational stability
prediction and Computational Alanine Scanning – Anne Goupil / A.
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
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
Automatic Creation and Validation of Pharmacophores derived from
Receptor-Ligand Complexes Tien Luu / A. Stevens
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
Discovery Studio 3.00 /Pipeline Pilot 8.00 Integration -
Anne Goupil / A. Stevens
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.
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: