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Eisai to Acquire Global License to ChemAxon Software for Drug Discovery Infrastructure

1st January

Patcore, Inc., an exclusive agency for ChemAxon in Japan, confirms the global licensing of ChemAxon’s JChem Cartridge for Oracle to Eisai Co. The database storage and search technology will be used by Eisai for the management of chemical structure information generated in discovery processes in Eisai’s global R&D organization.

Read more »
Linguamatics and ChemAxon Announce Project to Enhance Text Mining in Chemistry

14th December

Linguamatics and ChemAxon are pleased to announce that they are partnering in a new, path-breaking project funded by EUREKA’s Eurostars Programme.

Read more »
ChemAxon Moves to New European Headquarters

7th December

New location provides state-of-the-art environment for customer services, agile software development and continuing growth

Read more »
ChemAxon Adds Document Viewer for PDF Files to chemicalize.org

· 22nd November

Addition of a PDF Document Viewer to its open access chemicalize.org service. Researchers can now highlight and display chemicals mentioned in text PDFs such as patents and scientific papers, explore their properties and download as SD files for further study. Visit demo.

Read more »
The Utility of Cloud Computing

() · 16th November

ChemAxon’s David Deng presented a collaboration with GlaxoSmithKline (GSK) on cloud computing, in which 13,500 potential anti-malarial drugs have been made free available, hosted on EC2.

Read more »
Shionogi replaces chemical-structure-search system

3rd October

Patcore, Inc, an exclusive agency for ChemAxon in Japan, confirm the domestic unlimited licensing of ChemAxon’s JChem Cartridge for Oracle to Shionogi & Co., Ltd, Chuo-ku, Osaka.

Read more »
ChemAxon joint presentation with GSK: Deploying Global Informatics on the cloud

20th September

David Deng from ChemAxon presented a joint presentation with GSK Deploying Global Informatics on the cloud at the Bio-IT World and Cambridge Healthtech Institute’s Inaugural Bio-IT Cloud Summit. For the slides of the presentation please visit in our Library.

GSK’s Helium Rises to the Top

() · 15th August

Familiarity breeds contempt, it’s said, but not in the case of GlaxoSmithKline’s most recent tool for SAR analysis: Helium, which has the ubiquitous Microsoft Excel at its core, and received Bio•IT World’s Best Practices Award in the Knowledge Management category this year.

Read more »
Call for participants and announce program: ChemAxon's 2011 UGM: September 27-28, San Diego, CA

5th August

We are announcing the program and calling for participants for ChemAxon’s 4th US User Group Meeting (US-UGM) which will take place in San Diego, CA on September 27-28.

See the entire program

Read more »
IDBS and ChemAxon Extend Strategic Relationship

1st June

IDBS, a global provider of innovative data management, analytics and modeling solutions, and ChemAxon, a leading provider of cheminformatics software for the life sciences industry, announce today the extension of their relationship.

Read more »
Free Marvin Chemistry Extensions are now available in KNIME

26th May

KNIME together with its Life Science partners ChemAxon and Infocom is pleased to announce the release of the free Marvin Chemistry Extensions. These nodes are now available from the KNIME update site.

Read more »
Schrödinger Licenses Technologies from ChemAxon

13th May

NEW YORK, NY and BUDAPEST, HUNGARY (May 13, 2011) – Schrödinger and ChemAxon jointly announced today that the two companies have entered into an agreement to embed ChemAxon’s technologies in Schrödinger’s Seurat application.

Read more »
JChem and Marvin 5.5 launched

9th May

We are pleased to announce the launch of Marvin and JChem 5.5, the major new features are listed below along with links to download. JChem for Excel and Instant JChem will be released in the next couple of days.

Read more »
ChemAxon launches ‘live’ chemistry in Microsoft SharePoint™

12th April

Budapest, Hungary, 12 April, 2011 – ChemAxon, a leading provider of chemistry software for life sciences, announces the release of JChem for SharePoint to fully enable chemistry within Microsoft’s SharePoint™ platform. The launch includes Web Parts and Custom Lists for chemical editing, search and property prediction. The development has been in conjunction with pharmaceutical R&D partners.

Read more »
AKos GmbH Announces the Adoption of ChemAxon Marvin Java Applet as Structure Editor in CWM Global Search

9th February

STEINEN, Germany, February 8, 2011 — The compactness of the Marvin Java Applet and it’s capability to be launched in a separate resizable window, allows CWM Global Search on computers with small screens such as laptops, NetBooks or MacBooks.

Read more »
Thomson Reuters and ChemAxon Partner to Help Speed Drug Discovery for Life Science Researchers

4th January

For the first time ever, R&D end users can search and analyze Thomson Reuters trusted Markush chemical structures and patents with ChemAxon’s cheminformatics applications to streamline workflow productivity

Read more »
Call for papers announced: ChemAxon European UGM, May 17-18th, 2011, Budapest, Hungary

8th December

We are calling for papers for ChemAxon’s 2011 European User Group Meeting, to be held on Tuesday and Wednesday, May 17-18th at Danubius Health Spa Resort Margitsziget in Budapest. Satellite meetings include Developer and End user training and Markush Forum.

Read more »
JChem and Marvin 5.4 launched - 64 bit, multi-threading, enhanced transformations, R-group ordering, new predictor plugin, ECFP, expanded reaction library, disconnected MCS

6th December

We are pleased to announce the launch of Marvin and JChem 5.4, the major new features are listed below along with links to download. JChem for Excel and Instant JChem will be released in the next weeks.

Read more »
Gridlogics announces launch of Patent iNSIGHT Pro – CHEMPAT™ Edition

15th November

November 15, 2010, Pune, India – Gridlogics, a patent analytics solutions specialist and the company behind Patent iNSIGHT Pro, announced that it has partnered with ChemAxon to enable a specialized edition of the product (CHEMPAT™ Edition) suited for Chemical and biopharmaceutical companies. The CHEMPAT Edition combines the Patent research, analysis and reporting capability of Patent iNSIGHT Pro with the Chemical extraction, storage, management and search capabilities of ChemAxon’s products JChem Base and Name to Structure.

Read more »
chemicalize.org gets search and goes beta

3rd November

We have a launched a major upgrade of chemicalize.org with new features and upgrades to existing features. chemicalize.org now provides a search interface that lets you browse and discover molecules in our database of previously chemicalized webpages and structures.

Read the changes below or head over to chemicalize.org to try it.

Read more »
National Institute of Advanced Industrial Science and Technology (AIST) adopts ChemAxon JChem Base for Japanese Consortium for Glycobiology and Glycotechnology Database (JCGGDB)

2nd November

November 2, 2010 Tokyo, Japan and Budapest, Hungary, Patcore Inc. and ChemAxon, a leading provider of cheminformatics software for the life sciences industry, announce the licensing of ChemAxon’s JChem for the Japanese Consortium for Glycobiology and Glycotechnology Database (JCGGDB).

Read more »
David Spender - IN MEMORIAM

19th October

David Spender, a chemist and colleague passed away today following several months of treatment for pancreatic cancer. David has worked throughout the cheminformatics industry and we were fortunate in being able to enjoy his professionalism, experience and humor in these years.
This is a very sad and premature loss to his friends and family as well as to the cheminformatics society.
He will be greatly missed.

Alex Drijver
CEO
ChemAxon

A tributes page has been set up by the local newspaper for David’s area, to see please visit this link

International Union of Crystallography chooses ChemAxon Name to Structure technology

21st September

The International Union of Crystallography (IUCr) has signed an agreement with ChemAxon to use their “Name to Structure” and “Marvin” software to help ensure the quality of the IUPAC nomenclature in articles published in IUCr Journals.

Read more »
Riken Institute adopts ChemAxon Instant JChem for RIKEN Program for Drug Discovery and Medical Technology Platforms project chemical data management

1st September

Yokohama, Japan and Budapest, Hungary, RIKEN and ChemAxon, a leading provider of cheminformatics software for the life sciences industry, announce the licensing of ChemAxon’s Instant JChem for the Drug Discovery Computational Chemistry Platform Unit (SSBC) at RIKEN. The software is to be used to support registration processes and for data distribution and analysis.

Read more »
Broad Institute acquires license to all ChemAxon products and deploys across Chemical Biology Platform

19th August

Compound registration, structure search and computed properties rolled out.

ChemAxon announced today that they have entered into an agreement with the Broad Institute of Harvard and MIT, which will license ChemAxon’s platform, discovery toolkits and desktop applications for institute-wide use. Broad will support their legacy small molecule registration system and other functionality across their Chemical Biology Platform with ChemAxon’s technology.

Read more »
ChemAxon Distributes JChemExtensions worldwide

, · 30th June

INFOCOM Corporation, a ChemAxon Integration KNIME partner, today announced that ChemAxon has started distribution of Infocom’s “JChemExtensions for KNIME”, which allows researchers to work with chemical structure data using ChemAxon’s software tools such as Marvin, JChem, Standardizer and Calculator Plugins, on the KNIME open source workflow platform.

Read more »
Feature parade for Instant JChem 5.3.4

22nd June

A new version of Instant JChem has been released. Version 5.3.4 adds features like support of multiple database schemas for Oracle, improved startup performance, improved list management, better estimate of Markush library sizes and much more.

Learn more about this release »

US UGM (Boston, Sept 14-15): Call for abstracts opens

10th June

User Group Meeting: September 14-15th Training day: September 13th, Markush Forum: September 16th

ChemAxon’s 3rd US User Group Meeting (US-UGM) will be held at the Omni Parker House in downtown Boston, MA.

Read more »
2010 EUGM Archive opens - see video and download all presentations

9th June

Presentations and video from ChemAxon’s 6th European User Group Meeting (E-UGM) are added to the UGM archive.

The Archive includes original presentations, posters and video of the event as well as a meeting report from Wendy Warr.

Visit Archive

Searching PubChem and ChemSpider from the MarvinSketch canvas

8th June

In the 5.3.4 release we introduce a search available directly from the MarvinSketch canvas to search with the current molecule against public structure searchable databases.

Currently ChemSpider and PubChem are supported.

New My Evaluations page opens

9th May

We have added the capability for forum registered users to generate their own evaluations for ChemAxon products. We have broken down functionality to the following products/product areas:

  • Instant JChem
  • JChem for Excel
  • Platform IT
  • Name to Structure
  • Library Enumeration
  • Discovery Toolkit
  • IP & Markush

All evaluation licenses are free and valid for 2 weeks.
Visit My Evaluations

ChemAxon expands office facilities - Yvonne Martin inaugurates

9th April

In response to steady increase in business and a broader service offering, ChemAxon has expanded office space, approximately doubling the available facilities at the Budapest head office.

Read more »
Structure Drawing Adds Search Flexibility to CRC Press’ Combined Chemical Dictionary

23rd March

BOCA RATON, Fla.—March 19, 2010—CRC Press, a member of the Taylor & Francis Group, an Informa Business, is teaming up with ChemAxon, a software solutions provider for cheminformatics, to bring a flexible new search function to The Combined Chemical Dictionary Online (CCD) – an extensive chemical database containing entries on more than 500,000 substances.

Read more »
European UGM program announced

16th March

The program is now available for ChemAxon’s 2010 European User Group Meeting which will be held on Wednesday and Thursday, May 19-20 at the Danubius Hotel Gellert, Budapest, Hungary. The meeting will preceded by a training day on May 18th and followed by a Markush Forum on the morning of May 21st.

Read more »
Marvin 5.3 launched

4th February

Major new features:

  • Structure Checker add-on, a tool for detecting molecule features or drawing errors.
  • New Template Library handling: custom directory import, hierarchical system.
  • Enhanced quality of Marvin objects embedded in MS Office documents
  • Sprout drawing
  • Bracket drawing tool and bracket editing
  • Multirecord file import to canvas
  • Import of VMN files and import of images using OSRA.
  • CDX file export
  • Structure search in ChemSpider available from the menu

Download

Release Notes

History of changes

JChem 5.3 launched

4th February

Major new features:

  • Structure Checker add-on, a tool for detecting molecule features or drawing errors
  • Pre-regeneration ability of JChem Tables
  • Homology groups supported on the query side
  • Support of Markush DARC – used by Thomson Reuters Merged Markush Service
  • Markush support in JChem Cartridge
  • Relational data handling in JChem Web Services
  • Ajax example: Spreadsheet sorting by columns
  • Reactor: pre-filtering reactants speeds up enumeration
  • Sphere Exclusion and K-Means clustering methods in JKlustor

Download

Release Notes

History of changes

Pfizer selects ChemAxon's Markush platform

21st January

Pfizer globally licenses ChemAxon’s platform for Markush structure searching and enumeration

Read more »
The Edge and ChemAxon collaborate to add chemistry to their Morphit spreadsheet technology.

18th January

Morphit – the high productivity spreadsheet for pharmaceutical research is enhanced by the addition of a chemistry plug-in allowing chemistry data to be captured and analysed with ChemAxon’s JChem and Marvin technology

Read more »
Call for papers opens

17th January

ChemAxon’s 6th European User Group Meeting (E-UGM) will be held on Wednesday and Thursday, May 19-2th, at the Danubius Hotel Gellert, by the Danube, in the heart of Budapest.

The UGM will be preceded by developer training on Tuesday May 18th.


Missing: Peter Csizmadia

30th December

Péter Csizmadia, a physicist, a programmer and a mountaineer, along with 3 other Hungarians (Kata Tolnay, Vera Mikolovits, and Balázs Pechtol) disappeared in China’s Sichuan near the Ren Zhong Feng peak of the Himalayas probably in the early morning of October 23, 2009. A large part of a glacier fell off causing a huge ice/stone avalanche that covered the valley where they had their camp for the night. Neither their bodies nor their belongings were found by the ground and helicopter rescuing teams. There is no realistic hope any more that they will be found alive.

Péter was one of the founders of ChemAxon and he developed the early versions of Marvin. In ChemAxon he is known as the father of Marvin. Whilst he kept close ties with the company and was always available when we needed him, in recent years he pursued his career as a research fellow at the KFKI in Budapest. His other passions were mountaineering and photography.

We all share in the deep sadness of this tragedy, and our sympathies go out to the families.

A blog has been opened in memory of Péter.

Alex Drijver
CEO
ChemAxon

2009 US UGM - Archive opens

6th December

2009 US UGM - Archive opens

ChemAxon’s US User Group Meeting archive is opened.

The archive includes all available presentations to download and review.

Visit archive

Summary from Yvonne Martin’s Meeting report:
(Read full report)

“The meeting highlighted the extraordinary talent and hard work of the ChemAxon staff in making their software so powerful and yet so easily integrated into many different applications. In addition, it provided hints of fundamental changes that will come to end-users of cheminformatics tools. For example with ChemAxon tools embedded in workflow tools, it is much easier for computational chemists and expert users to perform a sequential variety of tasks for some purpose. However, such a workflow can be encapsulated and deployed to bench chemists.

Of course the web has changed the way that many things are done. ChemAxon has not ignored this trend and increased its presence in this area. The URL fields data type in Instant JChem supports accessing web resources within a desktop application, returning text or an image. Web browsing of the scientific literature could be transformed by functions such as seen in the prototype Chemicalize.org, which finds chemical names within a web document and shows the corresponding structure with a link to property predictions.

ChemAxon’s work to integrate into SharePoint will enable full cheminformatics capabilities within Sharepoint Blogs, Wikis, and discussion boards. This clearly could transform the way that discussions within a team occur.

In short, this was an exciting meeting that showed solid progress, fruitful collaborations, easy integration of ChemAxon software and suggestions of exciting capabilities in the future.”

JChem for Excel 1.1.2 launches

26th October

JChem for Excel 1.1.2 released.

Major new features:

  • Library enumeration
  • Marvin .NET (beta) GUI
  • 2D cleaning

  • Structure canonicalization
  • Structural framework functions
  • API made available

Visit history of changes

Download

Instant JChem 3.0 launched

26th October

New version improvements in these areas.

  • URL Fields
  • Browser widget
  • Enhanced schema editor
  • Support for database views
  • Controlling editability
  • Row level security
  • Improved printing
  • Improved structure renderer
  • Reaction based enumeration
  • Additional similarity metrics

New 3.0 features listing

Download

Try online – Java Web Start

2009 European UGM - Archive opens

26th October

ChemAxon’s European User Group Meeting archive is opened.

The archive includes all available presentations to download and review.

Visit archive

Conclusion from Wendy Warr’s meeting report. Read full report

How does this meeting differ from other user meetings? Recently I have been to two user meetings where the underlying theme was “ELN ELN ELN”, so it was interesting to sit through two days of a programme that was not ELN-centric. The ChemAxon meeting is also less marketing oriented than a typical American user meeting and there is less business jargon. Some of the talks did have lengthy lists of features but the underlying approach is, in general, centred on computer science and computational chemistry.

As ChemAxon seeks to become a more “serious” contender in the cheminformatics marketplace, I do hope that it will not throw the baby out with the bath water and lose the very special characteristics that its faithful customers appreciate. Alex Drijver says that ChemAxon aims to retain its existing virtues but to develop a more confident and serious business face as well. He speaks with the confidence that one would expect of a CEO but neither he nor the other speakers sound like smooth or slick marketing executives. I hope that ChemAxon will not begin to learn marketing-speak: currently it is a pleasure to find that no one at this user meeting thinks that “levverage” (sic) is a verb. Gradually ChemAxon is moving towards “enterprise strength” (another bit of business-speak you do not hear at this user meeting) but it still seems to be doing so in an approachable way. Customers clearly do not see ChemAxon as inflexible, arrogant or monolithic.

Are there any negatives? The variety of material covered in this user meeting did make me think that ChemAxon wants a finger in every pie (except perhaps a ChemAxon ELN). Could this lead to the developers being over-stretched? I hope not. Thus far the company has shown how fast it can grow its new ideas; it has low overheads compared with its major US competitors and it has taken on more developers in the Czech Republic and India. Thus far it has a good record for delivering on its promises. No company can afford to stay still; ChemAxon still seems to be managing the balancing act pretty well and it is remarkable how its revenues are increasing, despite the very difficult market conditions. Competition among vendors is good for users and I am positive about ChemAxon?s plans for the coming year.

Power query in Marvin

26th October

A complex query in Marvin, all query features can be processed by JChem Base and JChem Cartridge.

Features shown:

  • lists / not-lists
  • query atom types (A – any, Q – hetero)
  • query properties (aromatic, aliphatic, unsaturated, valence, substituent number, implicit/total hydrogen number, ring atom)
  • stereochemistry
  • abbreviated groups

Marvin & JChem 5.2 released

26th October

5.2 JChem & Marvin has been released. Instant JChem 2.4.3 (includin the 5.2 JChem) is also made available.

New product: Metabolizer. Predicting all and major metabolites as well as metabolic stability (info).

New add-on: Web Services Server for Web services integration (info).

New Calculation Plugins: Flexible 3D alignment for multiple molecules (info), structural framework calculation including Bemis-Murcko (info).

New features selection
Marvin
: True transparent structure painting, Chemical Terms editor support, homology group drawing. Marvin history of changes

JChem: New .NET API, Repeating units and homology groups query support, substructure and full fragment searches are 2x faster, new AJAX search implementation/code example, polymer search and storage improved support. JChem history of changes

Markush structure representation and storage - latest

26th October

Marvin and JChem 5.2 has improved support for drawing and storing Markush structure features.

Markush features handled in storage, search & enumeration:

  • R-groups (nesting to any depth)
  • Atom lists, bond lists
  • Position variation bond
  • Link nodes
  • Repeating units
  • Homology groups (aryl, alkyl, etc.) – built-in and user-defined

Overview of Markush Project (ppt)

Markush search example

Click on Marvin icon to see all Markush features within a single structure or visit this link

CDX file support

26th October

CDX, the native file format of ChemDraw, is now supported. The support allows users to open CDX files into all ChemAxon products.
Although all features are not supported in this initial implementation, all major features can be handled and development is ongoing.
User manual, Download Marvin.

Instant JChem 2.4 released

26th October

Instant JChem 2.4 has just been launched. This release brings a large number of usability improvements as well as further enhancing Instant JChem’s scalability and integration within enterprise platforms by adding support for the JChem Cartridge for Oracle.
Support for the cartridge allows;

  • searching performed by cartridge reduces memory utilization on IJC client allowing larger databases to be searched
  • simplifies migration from other architectures such as ISIS or Daylight
  • simplifies access of IJC data from other applications using SQL
  • allows access to data already in JChem cartridge from IJC

For version 3 (Q1 2009) we will be bringing a 3 tier architecture further enhancing scalability and integration. This will lead to the ability to develop web applications and web services around the Instant JChem architecture.

For more details of the upgrade please see the Release notes. To download or run using Java Web Start see this page

ChemAxon Pipeline Pilot Components latest featured in Accelrys Newsletter

26th October

The latest development of ChemAxon’s Pipeline Pilot components are overviewed for Nov 2008 Accelrys Pipeline Pilot Newsletter.

Visit Overview

Recent Pipeline Pilot presentation at ChemAxon US UGM

Download Component collection (free & open source)

Marvin / JChem 5.1 launched

26th October

Marvin new features: (see details and history of changes)

  • IUPAC Name import: converting IUPAC names to structures.
  • OLE 2 support: improved support of pasting Marvin Sketch objects into MS office documents.
  • Chemical Terms: available from Marvin in command line, API and can be used in Java scripts (in applets) for dynamic interaction with MarvinSketch.
  • Accelerated startup.
  • Improved logP calculation algorithm.

JChem new features: (see details and history of changes):

  • Position variation bonds in queries and Markush structures.
  • New architecture for tautomer duplicate handling, allowing more correct and faster operation.
  • New search options in JChem Base

Fall Newsletter released

26th October

We launch our quarterly Newsletter to keep you in touch with the latest developments and events.

In this issue

  • Markush structure storage & search
  • IUPAC Name to Structure Generation
  • Instant JChem; Cartridge & server support
  • New: JChem for Excel
  • Events & dates for your diary
  • Goodies
  • Housekeeping: New license file system

Visit Newsletter

Inaugural US UGM, Aug 7-8, Boston, MA

26th October

The presentation Archive of ChemAxon’s 2008 Inaugural US User Group Meeting are posted.

“In summary, the first ChemAxon US User Group Meeting provided attendees with both a view of the existing and new capabilities of the company’s software but also inspiration from other users as to how the software might be used in their own institution. Hopefully the next user meeting will diverge from the emphasis on structure-data integration to highlight user experiences with the powerful capabilities in Reactor, the Calculator Plugins & Chemical Terms Language, Screen, and Fragmenter. None-the-less, the experiences reported by users and the advances reported by ChemAxon support the view that ChemAxon provides “The Solution” for many cheminformatics problems.”

Extract from Yvonne Martin’s meeting report.

Visit main Archive

Meeting report by Yvonne Martin

ChemAxon/SciTegic Pipeline Pilot component collection version 1.2

26th October

Based on co-development with SciTegic/Accelrys the version 1.2 component collection is launched , the new release extends the functionality available and includes compatibility for the latest Marvin/JChem (version 5).

Available Pipeline Pilot component collection for ChemAxon products:

  • Standardizer
  • Chemical Terms filter
  • Reactor
  • JChem chemical database: insertion, search and retrieval of structures
  • Calculator plugins (HBA, HBD, Isoelectric point, logP, logD, pKa, Polarizability, Refractivity , TPSA, Burden eigenvalue descriptor (BCUT))
  • Marvin sketcher and viewer
  • Major microspecies (major protonation form)
  • Microspecies distribution

Download component collection

Visit recent presentation at SciTegic UGM

2008 European UGM Archive opened

26th October

The presentation Archive of ChemAxon’s 2008 European User Group Meeting are posted.

“As ChemAxon seeks to become a more “serious” contender in the cheminformatics marketplace I do hope that it will not lose too much of its informality and friendliness. The users will not want it to lose its justifiably high reputation for support. ChemAxon aims to retain its existing virtues with a more confident and serious business face. Alex Drijver talked of the company entering puberty after its 10 years in business. Puberty can be a trying time. Small, and newer companies have an advantage when it comes to responsiveness. Smaller companies are more agile than lumbering great corporations. As companies grow in size and age they have to face all sorts of new challenges. Fans love to stick up for the little guy; Microsoft and MDL never scored highly in the popularity stakes. I do have high hopes for ChemAxon and I wish the company well. It will be interesting to watch its progress over the next 10 years.”

dextract from Wendy Warr’s meeting report

Visit main Archive

Meeting report by Wendy Warr

Human Beta1 Alcohol Dehydrogenase ligand interaction

26th October

MarvinSpace provides visualization tools to allow researchers to focus on the most relevant aspects of protein-ligand interactions.

Accurate and smooth surfaces combined with various drawing and coloring modes help identify the complimentary shape between the HUMAN BETA1 ALCOHOL DEHYDROGENASE and its natural ligand.

The transparent protein surface allows us to ‘see’ into the deep binding pocket which is entirely filled with the ligand. The ligand’s surface is rendered with a mesh to allow to see the actual chemical structure.

For more information on the source protein see PDB entry here

libMCS v0.7 launched. Larger sets, faster and more chemical features

26th October

ChemAxon’s Maximum Common Substructure (MCS) clustering tool (LibMCS) automatically selects the largest and most frequently occurring scaffolds found in an arbitrary structure set. Structures are clustered around these scaffolds in a hierarchical manner.

Major improvements in the 0.7 release:

  • API made available (JChem 5.0.1)
  • Larger sets (100,000+) can now be handled
  • Faster operation
  • More chemical features are considered during clustering (keeping rings intact, match atom and bond type, formal charges etc)
  • Improved R-group decomposition and R-table visualization
  • Improved export options to allow user to reproduce/restore clusters in 3rd party/custom visualization, profiling or other applications
Marvin v.5 launched

26th October

Marvin – new features:

  • MarvinSketch: New, customizable GUI, chain drawing, improved editing of hydrogenized structures, improved branching in 3D, new graphics objects (parentheses, square brackets, braces, chevrons), text box contents can be aligned.
  • MarvinView: Spreadsheet-like view for displaying fields in SD and RDfiles.
  • Import/Export: IUPAC name generator, Gaussian Input/Output
  • Insertable Marvin OLE component into Office documents.
  • Calculator Plugins: Markush enumeration plugin added, IUPAC Structure > Name real time editing added (MarvinSketch)

Visit online MarvinSketch demo

Markush structure drawing, library definition and enumeration

26th October

Markush structures can be drawn in Marvin using R-groups and substituent lists.

Since the attachment point(s) of each substituent can be defined, it enables the correct representation of chemical libraries, which then can be enumerated within Marvin.

Integration of ChemAxon with TIBCO Spotfire DecisionSite

26th October

Brief presentation showing Marvin and JChem implementation with DecisionSite:

Screenshots/topics:

  • Rendering of structures using Marvin
  • Editing of structures using Marvin
  • Execution of structure based searching in JChem

Visit forum post

JChem Cartridge user reports "50 million molecules which works without any problem (and very fast!)"

26th October

Upon testing of large molecule sets, Lutz Weber of OntoChem reports

“…I have tested Oracle 10g with JChem (Cartridge) 3.1.3 using a database of 50 million molecules which works without any problem (and very fast!) on an 4CPU SGI Altix 330 12GB RAM machine. Now I wanted to compare this with a 3*4GB node cluster… The goal is to find an optimal set-up for very large databases…”

Visit Forum post

FAQ benchmark data:

ChemAxon 2007 User Group Meeting

26th October

Archive of the 2007 European meeting posted. Archive includes original presentations – where possible.

Presenting Users include: Affectis Pharmaceuticals, FMC Corp, Merck Serono, Teijin Pharma, Vertex Pharmaceuticals.

Presenting Partners include: Chemistry Logic, DeltaSoft, Genedata, Jubilant BioSys, KLEE Group, Synaptic Science, The Edge Software Consultancy, Virtua Drug

ChemAxon latest product development updates and new functionality announcements for: Metabolizer – new product, Markush patent structure search latest, IUPAC naming.

Visit Archive

Reaction drawing and auto-mapping

26th October

Reactions are represented using a “live” (non-graphical) reaction arrow, which identifies the components correctly.

The reaction can be mapped automatically (as shown in the image and associated structure file), but manual mapping of the atoms is also possible.

Instant JChem review in Chemistry World

26th October

Tobias Kind contributes a review of Instant JChem for Chemistry World magazine (Nov 07).

Download pdf

List and query handling in Instant JChem

26th October

Instant JChem 2.1 launched, lists and query management functionality added.

By managing your queries and their results, you can:

  • Create sets of favourite compounds
  • Combine results of multiple queries in powerful ways
  • Compare the result of a query to the previous times you ran it
  • Restrict the results of a search to the contents of a particular list

Peter Csizmadia et al reach summit of Hidden Peak (8068 m)

26th October

“Six climbers of the Hungarian K2 & Gasherbrum I expedition reached the summit of Hidden Peak (8068 m) yesterday at 2.00 p.m. (July 29th, 2007)” Zoltan Kemenczky told ExplorersWeb.

“Summiteers are Zsolt Eross, Anita Ugyan (female), Katalin Csollany (female), Hilda Sterczer (female), Peter Csizmadia and Istvan Tarjanyi. None of them used supplementary oxygen.”

Peter Csizmadia, (in picture), is a founder and lead developer at ChemAxon

libMCS v0.6 launched

26th October

libMCS v0.6 launched. The 0.6 launch sees major improvements in speed, memory use and sdf export option is added.

Maximum Common Substructure (MCS) clustering automatically selects the largest and most frequently occurring scaffolds found in an arbitrary structure set. Structures are clustered around these scaffolds in a hierarchical manner.

The GUI comprises a rich set of tools to help chemists analyze clusters:

  • Individual structures, clusters, subtrees and entire levels in the hierarchy can be browsed.
  • An R-group table of structures grouped in a cluster can be generated (Illustrated).
  • Structures can be filtered by properties included in the input set, filters can be combined, hits are color coded.
  • Distribution of various properties (e.g. activity) through clusters can be visualized as well as R-group decomposition.

2009 US UGM Meeting Report

7th October

2009 US UGM meeting report from Yvonne Martin posted:

“The meeting highlighted the extraordinary talent and hard work of the ChemAxon staff in making their software so powerful and yet so easily integrated into many different applications. In addition, it provided hints of fundamental changes that will come to end-users of cheminformatics tools.

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JChem for Excel launched.

16th July

ChemAxon launches JChem for Excel Introductory Webinar, July 21st, 11am EDT

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ChemAxon launches Marvin and JChem version 5.2; Web Services, native .NET API, homology groups, 3D Alignment and Structural frameworks.

15th April

ChemAxon launches Marvin and JChem version 5.2; Web Services, native .NET API, homology groups, 3D Alignment and Structural frameworks.

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