JChem Base, JChem Oracle Cartridge: Speed-up of combined searches

New improvements in our search algorithm result speed-up of search cases when chemical structure search is combined with non-structural criterion.

Combined, structural and non-structural compound query in SQL using JChem Oracle Cartridge  (JOC) can be defined as:

SELECT * FROM tableName WHERE jc_compare(‘CCC’, cd_structure, ‘t:s’) AND id<4000.

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MarvinSketch: on the way towards publication quality drawing

A new tool, the label editor has been introduced recently in MarvinSketch version 14.11.10.

This allows MarvinSketch users to edit and format labels easily. It effects the labels of atoms, abbreviated groups, R-groups, atom lists/not lists and also the introduction of an alias or a pseudo atom.

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More smart tools in Marvin JS

We do our best to create tools which are useful and help make your work faster and easier. One area we see much potential is in user interaction and simplifying tasks toward being intuitive. In the Marvin JS team we realized that sometimes the easiest ways are not the most trivial and complex problems can require complex solutions.

But what is the best way to illustrate or achieve tool behavior with actual chemists? Documentation, tutorials, consultancy? One solution we are exploring is an option to insert some “live hints” or guides into Marvin JS which appear as you draw chemistry. See below for 5 different examples of the guides in action but we are asking for your opinion here – does it feel natural, is it confusing, is there a better way? Does the hint reflect your idea about the physical behavior of the tool?

multicoordinatebond Drawing coordinate bonds


straightarrow Reaction & mapping


freehanddrawingFreehand drawing


eflowSingleArrowSelecting electron flow arrow arrow types


smartrgroup R-group handling


You can try these features in Marvin JS:

Tell us your opinion of this potential solve, is it relevant, does it work, how does it not work. Please take a minute to tell us if this is a good way forward by posting a comment.

Smart R-group tool in Marvin JS

Based on your feedback, we have created a brand new tool in Marvin JS to define R-Groups more efficiently. Instead of the “old” behaviour (selecting the context and pressing R + [SPACE]), this new solution requires a mouse or a finger only. Check this video tutorial, follow the steps, and please, share your thoughts with us.

Changes in the way we are releasing our software - faster and with a different sequence numbering

We are changing our release policy from July 8th from one of major releases every 4 months to a frequent release system whereby new releases will come out every week or so.

Details of the plan:

1) The next major release will happen on or around July 8th

2) From then on, we will make a new release every week which will include both new features and bugfixes.

3) Hotfix releasing will be discontinued since hotfixes will be added to the frequent feature releases. Because of this it might sometimes happen that a release will only include bug fixes.

4) To make it easier to follow which version we are on, the version numbering will be date based in the format yy.mm.dd For example 14.7.7 for the release of a build on July 7th 2014

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Creating and understanding Markush libraries: Markush Editor

Markush structures are widely used in combinatorial chemistry and patents to define large chemical spaces. However, handling complex Markush structures (containing hundreds of fragments) with existing structure editors, including Marvin, is extremely challenging.

While ChemAxon already has a useful technology in our Markush Viewer, the technology base is old and not a good starting point to add the extensive editing capabilities we were thinking of. We also wanted to include some of our Markush search/canonicalisation tech, in the background to make the editor chemically and Markush ‘aware’. So we started from scratch revisiting the topic with completely fresh eyes, a strong image of where we want to go and a fair list of use cases to base our works on.

We hope you agree that Markush Editor will be a valuable tool for IP experts and chemists to draw and edit complex markush structures faster and with more confidence than ever before.

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Solubility prediction - ChemAxon's Solubility Predictor

Aqueous solubility for organic compounds is one of the most important physico-chemical properties in modern drug discovery and has long been among our plans. Being a property that is hard to model, providing a tool for prediction, in a fast and accurate way, has not been an easy task and so we are pleased to announce our solution in the latest 6.3 release.

ChemAxon’s Solubility Predictor is able to predict aqueous intrinsic solubility and pH-solubility profile for molecules. An example below shows the prediction results for the acebutolol molecule.

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tl, dr May

Hi Folks!

This month was all about delivering another successful UGM for us, but there is also plenty of other noteworthy things have happened around us. Enjoy this latest selection.

Carbon Fiber production is scaling up to meet demands
Things around the “island of stability”
Who’s the most R&D productive pharma?
Proteome map ready
AZ – Pfizer dating is over
Check out our latest UGM

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Japanese Chemical Name Support Has Arrived


Hello Everyone,

You probably know that ChemAxon’s Name to Structure (N2S) can recognize both English and Chinese names. (If you didn’t know about our Chinese Name to structure (CN2S), look here.) Why do we support both languages? Because Chinese and English patents are No. 1 and 2 in the world. The figure below shows the number of patents filed at the top 5 patent offices from 1980-2012.


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tl, dr April

Hi Folks! So many exciting discoveries have happened and surprising news has come to light in April, it was really hard to decide what to cover here. This is really only the top few on my list. Hope you enjoy, and will learn more about them!

Exciting News on Graphene Front
First real “Inorganic Grignard Reagent” Prepared
Perovskites for Photovoltaics & Lasers
Once Again: Nanoparticles for Enhanced Drug Delivery
Multibillion Dollar Deals Between Pharma Giants

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