April 10, 2018

KNIME workflows for downloading of MolPort data for offline usage

MolPort provides a number of ways to access data and catalog information on commercially available compounds: the MolPort website, the MolPort downloadable database, MolPort web services (API). With web services you can instantly check the current stock level information for MolPort compounds from your software application, Microsoft Excel, Optibrium StarDrop, Pipeline Pilot or KNIME nodes.

A certain type of data analysis, like filtering by specific parameters, diversity selection, virtual screening or docking, require you to have full data locally. Full data download and its preparation for use require a certain amount of effort on the user’s side. Following MolPort user requests, we created two examples of workflows that automate this process using KNIME. Now you can get to MolPort data in KNIME easier.

The first workflow named “LoadAllMolPortMolecules” does not require data access credentials. With this workflow you get chemical structures of all available compounds, their MolPort IDs and website links to acquire further information. You can easily share this example with colleagues to provide them with a fast and easy way to access MolPort data. The process of downloading the complete data set (100 MB) and loading it to KNIME may take less than 5 minutes and requires 2 GB of space on your hard drive. All you must do is set up a folder for local file storage.



The second workflow, named “LoadMolPortExtendedData”, allows you to acquire extended information version of data. In this case there are multiple downloadable files.. For each compound additional data includes the largest available  stock amount, the fastest shipping time, price ranges for 1mg/5mg/50mg, whether it is available as a Screening Compound or a Building Block, the QC type, the InChI and the InChIKey. Access to such data is also free, however requires use of credentials. To get yours, simply send a message from your corporate email address to customerservice@molport.com. Then set up the second workflow example to get full data version.




Some companies have a restriction for FTP access. You may need to work with your system administrator to add MolPort FTP location to allowed list. Alternatively, contact us to get access to files through HTTPS.

Both workflows contain descriptions and are compatible with KNIME version 3.3 or later.

Files for download:


LoadAllMolPortMolecules.knwf
LoadMolPortExtendedData.knwf

December 18, 2017

MolPort 2017 Christmas & New Year's Holiday Shedule

MolPort offices will be closed on December 25th and 26th for Christmas, as well as January 1st January for New Year's Day.

Please note: Holiday schedules vary by supplier. Please, review these shipment cutoffs for our major suppliers.





We look forward to assisting you with all your compound ordering needs in 2018! Happy Holidays!

May 3, 2017

Drawing Tricks for More Effective Substance Online Ordering - Webinar presentation

On April 27th MolPort and ChemAxon held a joint webinar, aimed at helping scientists master the MolPort chemical structure search interface. ChemAxon's Marvin JS is a state of the art chemical structure editor that is integrated into MolPort’s web interface to query the commercially available compound space. In the course of this webinar, you will be walked through the basic structure search editor interface on www.molport.com, will pick up productivity tips and advanced structure query capabilities.

 View the recorded webinar video presentation:


Visit  Marvin JS user guide and query strategies for additional documentation.

April 26, 2017

Structure Search User Interface Gets a Number of Small but Important Improvements

We Part with the Marvin Sketch Applet Editor


We removed the Java Applet structure editor from our website. Browsers have poorly supported Applets in corporate environments; they were slow to load and the IT industry, as a whole, has moved on to JavaSript and HTML5 technologies for a number of reasons. The newer and quicker ChemAxon's Marvin JS editor has been available on our website for some time already and our users overwhelmingly favored it over the applet version of the editor. You can still use the ChemAxon Marvin Sketch applet installed on your PC, if that is your preferred editor, and copy-and-paste the structure to the editor on the MolPort structure search website.

Building Structure Queries


We made several changes to the page, where you start your structure search. This is it’s current version:




You may notice that the editor is now larger in comparison. We moved search filters and options to the lower part of the page. Recent and saved queries will be listed below the filters and options.
Notice that there are now 3 tabs above the editor:

  • Draw Structure
  • Convert to Structure 
  • Load from File

Draw the Structure


It is the first tab shown, when you load the page. Here you can graphically compile the structure query.

Convert to Structure


This is the tab, where we introduce you to some nice new functionality. Your searches by chemical names now result in exact compounds you are looking for. However, not only does this compound has to be in our database, we also need to have the particular version of the name you used stored in it. That is how text search engines work. And since chemical names can be complex, chances are you may miss the compound. Structure search is a much more powerfull and robust way to find the needed compound. And it offers other noteworthy benefits: you can search for close analogues of the compound, for example. Drawing the structure may be tedious for larger compounds, however.

Now you can start with a compound name, convert it to a structure, modify the structure, if needed, and proceed to run a structure search in the MolPort database. Currently we support the following data input types for conversion:

  • IUPAC name
  • Synonyms and traditional names
  • InChI
  • SMILES
  • SMARTS

We use a combination of database lookup and name-to-structure conversion strategies to convert the text input to a chemical structure. While it works for most valid chemical names, it is not always successful.

Example


Here is an example compound and various names, i.e. identifiers, that can be successfully parsed to chemical structure:
2,3,6,9-tetrahydro-1H-purine-2,6-dione structure
  • 2,3,6,9-tetrahydro-1H-purine-2,6-dione
  • 1,3-dihydropurine-2,6-dione
  • 1H-Purine-2,6(3H,7H)-dione
  • 2,3,6,9-tetrahydro-1H-purine-2,6-dione
  • 3,9-dihydro-1H-purine-2,6-dione
  • 3,9-Dihydro-purine-2,6-dione
  • Xanthine
  • O=c1[nH]c2[nH]cnc2c(=O)[nH]1
  • 1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)

Load from File


As the name implies, in this tab you can upload a saved structure or query to the tool.

Better navigation


We improved search-related navigation as well. First of all, when you go back from search results to the structure editor and query building, the last searched structure will be automatically loaded in the editor. That way you can adjust the query to make it more specific or broaden it.

We also improved the breadcrumb navigation from Search to Molecule. A typical navigation path when searching is:


Home > Draw Structure > Search Results > Molecule



Now you can navigate from the Molecule back to the Search Results, to see other search results, or to Draw Structure, to edit the query structure.

April 18, 2017

Launching an Automatic Update Site for MolPort KNIME Nodes

MolPort provides a number of ways to access data on commercially available compounds and their catalog data: the MolPort web portal, a downloadable database, web services (API). With web services you can instantly check the latest stock level information for MolPort compounds from your software application, Microsoft Excel, Optibrium StarDrop, PipelinePilot or KNIME.

Starting today, MolPort KNIME Nodes are available from the traditional KNIME install/update website. This will not only make the installation process much easier, but will also keep them up-to-date automatically. Just add https://www.molport.com/knime/ to the list of update websites.

Here is how you do it:

 

Open KNIME, then click Help menu, select Install New Software.
Paste https://www.molport.com/knime/ into the Work with field.
Press the Add... button and then save the update resource with a name of your choice. We have used MolPort nodes as an example (see figure below).



Check the box for MolPort KNIME Nodes or just use Select All below to install or update the existing version of MolPort Nodes.




Press Next > or Finish and follow the next installation steps.

The download size does not exceed 10Mb for the current version, but the installation process usually takes up to 5 min. When the installation is complete, KNIME will prompt you to restart the application.




 After the restart, you can find MolPort Nodes in your local Node Repository.




 Please find here more information about MolPort KNIME nodes here.

We would appreciate your feedback and suggestions regarding this feature very much. In case of any question regarding the installation process or the MolPort nodes themselves, you are welcome to get in touch with us, using the contact form.

April 12, 2017

Specify Sample Amount Individually for Each Item in List Search

MolPort List Search is a tool, available on the MolPort homepage, which aims to simplify the sourcing of a list of reagents or HTS samples. If you have compound structures in form of an SD file, a SMILES string list, or a list of MolPort ID references, you can do a quick search and optimize the shopping cart in real time.  See the List Search user guide. However, your specified sample amount applies to all compounds by default, which is great for HTS compounds, but may not be the optimal way to order building blocks.

On user demand, we added the feature to specify required sample amounts for individual compound in List Search. This is an example compound list:

Ref Nr
SMILES
Required amount, mg
Minimum acceptable amount, mg
LID2828
NC(C(O)=O)c1ccc2OCCOc2c1
300
100
LID1617
NC(C(O)=O)c1ccc(cc1)-c1ccccc1
300
100
LID2982
NC(C(O)=O)c1cccc(c1)[N+]([O-])=O
1000
100
LID4215
CC(C)(C)OC(=O)NC1CCCCC1N
800
100
LID3556
NC(C(O)=O)c1cccnc1
500
100
LID2377
COc1ccccc1C(N)C(O)=O
1000
100
LID4350
NC(C(O)=O)c1ccccc1F
700
100
LID2486
CC(C)(C)OC(=O)N1CCCCCC1C(O)=O
200
100
LID3074
NC(C1CCCCC1)C(O)=O
800
100
LID1893
NC(C1CC1)C(O)=O
100
100
LID2888
OC1CCCNCC1
300
100
LID2027
NC(C(O)=O)c1ccc2ccccc2c1
900
100
LID2759
CC(N)=N
200
100
LID0164
NC(C(O)=O)c1ccc(F)cc1
900
100
LID2173
NC(C(O)=O)c1ccc(cc1)C(F)(F)F
300
100
LID1590
Cl.NC(=N)C12CC3CC(CC(C3)C1)C2
800
100
LID4312
NC(C(O)=O)c1ccccc1Cl
300
100

Where:

Ref Nr
Your reference number for the compound.
SMILES
Specifies the structure of the compound.
Required amount
This is the desired sample amount of the compound in milligrams (other measurement units should be converted to milligrams to use this feature).
Minimum acceptable amount
Should the required amount of the compound is not available, you can specify the minimum amount you would be interested in. The sourced amount will be within the range of the Minimum acceptable amount and the Required amount. If the available sample amount is less than this quantity, the compound will be listed as unavailable.



Results of a List Search:



After specifying the desired amounts for separate compounds, you can either finish the ordering process online or generate a quote for creating a purchase order through your Purchasing Department.

October 27, 2015

MolPort API version 3.0 release

    Image result for molecules

We upgraded MolPort API to version 3.0.

We have made these changes (or visit API History of Changes):

  • New interface to allow chemical search by SMILES and SMARTS. We support exact, similarity, substructure and superstructure chemical searches.
  • Migration from XML to JSON data format because is much friendlier than XML, it is smaller, human readable and can now be used with all popular programming languages.

Not using Our API? Request access


About the API

  • The MolPort API is implemented as REST interfaces.
  • It is the easiest way to access current compound availability data from your workflow.
  • We have sample projects available in Java and C# programming languages to demonstrate the routines for API calls, data serialization, etc.
  • Take a look at the API Documentation to see the data structures that are used.

How to use? Two ways:

  1. Run SMILES or SMARTS structure queries on MolPort available compound database. Results will list SMILES and MolPort IDs of matching compounds.
  2. Load detailed compound availability information for a known MolPort ID (after structure search API request or if you downloaded our FTP database).


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