August 6, 2019

MolPort Inc. – now open for faster, more efficient chemical sourcing in the USA

MolPort is pleased to announce the opening of US-based MolPort Inc. to streamline compound ordering and payment for its many US customers.

By placing orders and processing payments via MolPort Inc., US-based customers will benefit from faster and more efficient chemical sourcing.

No More Customs Headaches

For US customers, understanding the various international customs rules and procedures is daunting, navigating chemical orders through the custom mazes can be frustrating and time consuming, and the smallest error can potentially hold up shipments or incur additional charges.
Orders placed through MolPort Inc. will have all the required international customs formalities taken care of, and so packages will sail through customs without delay or additional costs, saving time in preparing customs documentation and speeding the arrival of needed compounds.

Seamless Payment Options

As anyone who has tried to transfer money internationally from the USA knows, the process is complicated and more expensive than making a local payment.
With MolPort Inc., customers can pay for orders by cheque from a US bank, or they can get a quote online, provide a Purchase Order, and have it processed via MolPort Inc. – saving time and costs by avoiding an international funds transfer.

I’m a US customer: how do I interact with MolPort Inc.?

For optimal experience in placing your first order via MolPort Inc., we suggest that your procurement specialist gets in contact with us to open a new supplier account.

They will need to complete and provide the following documents/information so that we can add you to our procurement system:

o W-9 form
o Employee Identification Number (EIN)
o Tax-exempt status, if relevant

The MolPort Inc. W-9 form can be requested by email.

With MolPort Inc. open for business, our US customers can now enjoy faster and more time- and cost-efficient chemical ordering to better support their research.

For more information on MolPort Inc., please contact us 

June 11, 2019

MolPort real time order tracking and documentation

MolPort order tracking system allows the customer to gain insight into where their order is at any given point in time. From the time an order is placed until it is delivered. Be up to date with your order!

Order tracking service is available to everyone placing orders with us.

Registered users at have access to their complete order history and associated documentation.

Non-registered users are given access to their current order only.

Report sections:


No.1 Order tracking

An overview of the order, including the Billing and Shipping addresses and the download link of a spreadsheet with the detailed status for all ordered products.

No.2 Order status

As order transitions from one phase to the next, completed order process stages are marked green. Order may transition through following stages (actual order stages vary by order):

Order received
order has been received, registered and processed by MolPort
Compounds processing
compounds are being processed by suppliers (QC, packaging, shipment preparation)
package has been prepared and is waiting for the shipment
In transit
compounds are in transit from supplier to MolPort warehouse
In MolPort Warehouse
compounds have been received at MolPort warehouse and are waiting for the shipment or additional services
compounds have been received at MolPort warehouse and are being re-formatted in customer’s preferred format – re-weighing, sample splitting, DMSO solutions
compounds are shipped out to customer address
number of ordered compounds that cannot be delivered and have been cancelled from the order

No.3 Shipment summary

A shipment summary becomes available after a package is sent out to customer address. This includes:
  • Shipping courier name;
  • Shipment type (direct shipments from suppliers or single shipment from MolPort warehouse);
  • Tracking number (including a link to real time tracking at the courier’s website);
  • Packing list (packing data as Excel and SDF files).

No.4 Detailed delivery progress

The delivery progress report section list status of each ordered product. You can filter the product list by:
  • Supplier name;
  • Status (In transit, Shipped, Cancelled, Processing, in MolPort WH);
  • Ordered amount;
  • Ship out date.

We are able to follow and provide insight into the status of the order through its entire journey to the customer.

October 23, 2018

MolPort 2018 Christmas & New Year's Holiday Shedule

MolPort offices will be closed on December 24th, 25th and 26th for Christmas, as well as December 31st and January 1st 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 this year and in 2019!

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 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:


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, 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

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.


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 to the list of update websites.

Here is how you do it:


Open KNIME, then click Help menu, select Install New Software.
Paste 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
Required amount, mg
Minimum acceptable amount, mg


Ref Nr
Your reference number for the compound.
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.


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