Cheminformatics boosters: ChemAxon's partnership with IDBS

Jul 20, 2016János Fejérvári

ChemAxon, almost 2 decades ago, started as a toolkit company. We created easily integrable software that supports a wide range of technological environment and chemical format, while keeping it scientifically accurate. This business scope is changing lately. We started to focus on web-based applications providing an end-to-end solution for scientific workflows. Yet, partnering plays an important role in ChemAxon’s strategy. We believe that combining industry knowledge is able to push R&D forward, and that we can create an ‘out of the box’ solution reducing the burden on customer IT groups. Currently we have more than 100 partners worldwide, who have integrated ChemAxon technology. Read the whole post »

Java Applet Technology: The Past and Future and The End

Java Applet technology was a great tool to create nice and shiny applications that can be embedded into websites. It even had the ability to communicate with JavaScript through custom APIs. It was fun, people were happy.

But time went by, web based technologies evolved and the browsers adopted the changes. The plugin technologies (Flash, Silverlight, Java, ActiveX, etc.) were pushed back by JavaScript, CSS, and HTML5. The security issues in plugin based technologies did not help either by opening backdoors for malware and flooding the users with alert windows. Read the whole post »

Are we there yet?

About 18 months ago we published “MarvinSketch: on the way towards publication quality drawing”. Although the blog post was the trailing subsequence of the newly introduced label editor, the work has been started way before that and as you would expect it is going ever since. Now we believe the time is right to review the above statement and briefly summarise where we are.

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Did you know... ? A series of videos about ChemAxon's MarvinSketch and Marvin JS tools

MarvinSketch, our chemical editor, was among the first software ChemAxon started to develop. We have been continuously working to make it one of the most chemically-intelligent tool on the market. This is a great heritage that Marvin JS, our JavaScript based drawing tool could take over.

Throughout the development we added some really amazing features that can speed up your work. We wanted to throw some light on these smart details in a series of short videos.

Since mid October, every Thursday we post a brief tutorial to our YouTube channel, showing these hidden treasures in MarvinSketch and Marvin JS. At the time of writing there are 6 videos available, focusing on stereoisomer handling, keyboard shortcuts, quick peptide and reaction drawing.


We hope you will find these videos useful. Have a great time while watching.
If you have a thrilling idea to make video of, share with us and leave a comment down here.

Drawing complex biomolecules as easily as small molecules?

ChemAxon’s BioEditor

Recent exciting advances and innovations at the chemistry-biology interface has sparked us to bridge the gap between chemistry and biology and create our Biomolecule Toolkit.

The next step is to provide a biological sibling for our well established chemical editor, the Marvin. ChemAxon’s new, web-based BioEditor is to handle those complex macromolecules that are tagged by the relatively newly coined terms like “biologics, biologicals or biopharmaceuticals”, and also to add our industry-leading chemical intelligence to them.

To develop the closest editor to your needs, we would like to invite you to join us and meet at the starting line. Please help us to shape our new BioEditor by filling in this short, 5-minute survey.

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 For example 14.7.7 for the release of a build on July 7th 2014

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