Monday, December 16, 2013

About Instant Quote

Instant Quote is an end-to-end online solution for quote generation, ordering and tracking. It basically spans the whole procurement process that is painful and time-consuming and scientists hate it. It helps to find the best offer for a selected set of compounds and get them delivered to your lab.

We have developed Instant Quote to make life easier for scientists working on drug discovery projects or just ended up with a task to procure multiple compounds. We went through this a few times ourselves and we didn't like it. It takes so much time to contact and negotiate with suppliers, check the availability of compounds, try to calculate the best combination of products and suppliers, consider project deadlines, etc. To eliminate these painful parts of compound procurement was part of the Mcule mission.


The main benefits in a nutshell: Instant Quote eliminates e-mail communications from the whole process, thus it saves valuable time for scientists and procurement managers. Its unique algorithm calculates the best price and fastest delivery quotes in a minute. It can greatly reduce costs by comparing and optimizing compound prices, supplier discounts, small order fees, delivery costs, customs duties and reformatting options.

Here is how it works

If you have created a collection containing your selected compounds, just click on the orange Quote in the top right corner of collections. We will ask for some basic information required for quote calculation. For example, you can specify the preferred and the acceptable minimum amounts per compound, min. purity, max. delivery time and the supplier catalogs (grouped by stock information up-to-dateness) to be included in the quote calculation. You can also select the delivery format here. We can implement any customer-defined formatting option to Instant Quote in a few days and it will be displayed in your personal account. This can be particularly interesting for organizations frequently ordering in a special format (custom vials / plates, DMSO solutions, etc.). After filling out the Quote form, the best price and fastest delivery quotes will be calculated on-the-fly.

The algorithm

We developed a unique optimization algorithm which calculates the best price and fastest delivery quotes by comparing and optimizing compound prices, supplier discounts, small order fees, delivery costs, customs duties and reformatting options. Since the same compound is typically available from multiple suppliers and there are many parameters to consider during quote generation, the manual price and delivery time optimization could be very challenging even for a relatively small order. Additionally, requesting stock availability information is time-consuming especially when the information has to be requested by e-mail.

Our unique quote generation algorithm first automatically checks the stock availability for your selected suppliers. For almost 6M products we have access to the supplier's current stock levels that makes Instant Quote generation particularly reliable. In the next step, our algorithm finds the best product matches by minimizing the total price and the delivery time. Instant Quote generation typically takes 1-2 minutes even for thousands of compounds. After the optimization algorithm finishes the generated quotes will appear in the Quote list view.

The quotes

You first get a quick summary that we call the Quote list view. We list here the best price and the fastest delivery offers separately if the two differ. Click on “See details” to see the break down of the total price of the individual quotes and most importantly to fine-tune the quote by excluding particular compounds. After you selected the products you want to remove, click on the “Remove selected and recalculate” button and a new quote will be generated for the remaining products on-the-fly.

You can fine-tune the quotes based on Effective price, stock availability and purity information. After you finalized your quote, you can save it and export it in PDF or Excel formats. You can go back any time when you are ready to place the order. Optionally, you can specify a Purchase Order number and upload a PO file issued by your company / institution.

Order tracking

After you placed the order, you can track its status online by checking its unique URL. You can also request status updates and we will email you when the status of your order gets updated.


All your ordered products will be delivered to you as a single package and we provide complete EU and US customs clearance service (customs duties and taxes are paid by us). Mcule does not charge any hidden customs costs to its customers.

Test Instant Quote!

If you would like to test Instant Quote, you can freely access it until 31/03/2014. To get started, run a quick compound search on Mcule!

For more information on Instant Quote, please check our brochure and quick user guide.

Monday, December 9, 2013

What would you rather do?


If you like administration, please stop reading now.

Otherwise, find out more about Mcule's brand new product: INSTANT QUOTE. It will make screening compound ordering a joy.

Have a great day!

The Mcule Team

New features and new pricing

We are after a very interesting development period with several interesting features and changes, so here is what's new on Mcule:


1. New navigation menu

We revised our menu to make it more straightforward. Now we have grouped things as follows:

  • Hit Identification (things for virtual screening and library design - primarily based on Workflow Builder including pre-populated workflow templates, plus the Database Download page)
  • Lead Optimization (these are the popular 1-Click Applications for quick validation of chemistry ideas by docking, property profiling and toxicity checking plus the scaffold hop idea generator)
  • Find Chemicals (basic searching options for a single or multiple queries)
  • Collections (you know this one already - you can find all your search results here)
  • Instant Quotes (this one is new, see more below).

2. Instant quote

This is going to be a killer feature for compound procurement managers and it does what it says: Instant Quote generates price and delivery time quotes on-the-fly for a set of compounds. We have a nice brochure on this, and a more detailed blog post is coming soon on this feature. But here is a few words because we are really psyched about it:

You can make a compound selection by using some of the basic searching tools (Find Chemicals) or run e.g. a virtual screen, click on Quote, fill out a short quote form, and Instant Quote will generate a quote on-the-fly. And this is great! Here is why: we check the availability of all potential products that can be included in your quote on-the-fly (we have live and batch stock availability handlers for most of our suppliers). Plus (and this is the big deal) we solve a serious combinatorial problem of matching particular products to each of your selected compounds. This is not trivial, just think of 10 compounds, and 5 potential suppliers for each of them: that's 5 x 5 x 5 x 5 x 5 x 5 x 5 x 5 x 5 x 5 potential quotes, and our algorithm finds the ones with the best price and fastest delivery. And it works for even thousands of compounds. More on this soon...

3. 1-Click Application history (Lead Optimization)

We realized that 1-Click Docking and 1-Click Scaffold Hop are among your favorite tools. It is really easy to run these calculations and you get the results in a few seconds. However, in some cases it makes sense to see and compare multiple results and you might want to go back to one of your previous calculation. Now you can do that by clicking on the See history link at the top of 1-Click Docking and 1-Click Scaffold Hop.


We've got feedback that the previous pricing plans were too complicated, so we made them simple. We have put together three packages:


This is primarily meant for procurement managers and for those who frequently orders compounds and would like to optimize the costs (it contains Instant Quote). Plus, it is a great starter kit for modeling.


This package offers a reasonable package for small-, and medium-sized companies and academic research groups containing all the major features with very reasonable limits that enables to run several projects in parallel.


This is an enterprise solution: full feature set with a practically infinitive computational capacity. To see the full comparison, check out the Pricing page.

We still offer the Free package for those who want to test out our system. It has to be mentioned that docking target upload is now only available for subscribed users, but you can still use what you have already uploaded. On the plus side, we provide some 1-Click Application history for the free users as well.

If you want, you can request a 7-day trial including all major features.

I hope you will find the new features and packages attractive. But if you need something customized, you can always tell us, you know that. Contact us, and we will try to find the best solution for you.

Cheers from:
The Mcule team

Thursday, April 4, 2013

39 FDA drug approvals in 2012: everything is back to normal(?)

FDA approved 39 new drugs last year. This is great news no question about it. First thought is for celebration. Indeed. We needed this, and that's good news for all of us working in the drug discovery industry. Taking the large lay-offs, especially in the US, affecting thousands of people, I think this gives back something, at least the hope that this trend is about to change. But is it? I think it is worth digging a bit deeper and see what were the keys for this success. As demonstrated at BioSpring, 50% of the approved drugs were basically in-licensed by big pharma and 100% involved some SME (small/medium-sized enterprise) as a partner during discovery/development. What does this mean? If I would work for a big pharma company, I would probably not feel assured about future, as these numbers suggest as least for me that innovation is coming from SME and it is acquired or in-licensed by big pharma. One might also see trends like big pharma becoming investors and it is the SME that is focusing on discovery. I think this is normal and have nothing to do against great scientists working at big pharma. This is really not about which scientists have better capabilities, are they innovative or not, so don't take this personally. I think this is about what Steve Blank said once (can't remember the exact words, sorry). Imagine someone working at McDonalds coming up with the idea on a nice, sunny morning to prepare the burgers based on a new recipe. What would happen? He would be convinced to stop this non-sense and get back to work, and if he is still not getting it, he will be soon on the road to seek a new job (or starting his new shop based on the new recipe). I think there is an analogy to the pharma industry. Big pharma is good in execution, but that is probably not enough and is not the reason for the high number of new approved drugs on the market. Opinions?

Tuesday, April 2, 2013

Chemical probes vs. drugs

I came across this nice blog post on Chemical probes vs. drugs, and I think it touches an important issue. Several (mainly academic) groups identifying hits on novel targets with a suboptimal property profile. Some hits contain reactive functional groups or have an extreme lipophilicity. In these cases, it is always advisable to check the specificity of the hits as the compounds can actually bind to many targets and for example phenotypic effects might be due to other mechanism of action than the target in focus. Both reactive functional groups and high lipophilicity can be associated with selectivity issues and therefore they are less favored for further exploration. But there is a commonly used excuse for "ugly" compounds: that even though they are not fulfilling the criteria for entering into a drug discovery project, they are still useful "tool compounds" or "chemical probes". In the light of the cited Nature paper (very nice title btw: "Stay on target"), this should be reconsidered, as a chemical probe should be even more selective than drug candidates. I think this is worth remembering when dealing with results obtained with less nice compounds. Specificity should be tested at least on a basic level.

Wednesday, March 6, 2013

February Features

Here's the roundup of our latest features from the month of February.

Find chemicals more easily in our database
We've added the ability to search for multiple structures in our curated database. This feature is especially useful if you've saved one of your collections (or our whole database) for in-house processing and you would like to use our procurement services to easily purchase your results.

Additionally, the Find Chemicals feature is now available without first signing in, if you would just like to quickly check for a molecule.

Download everything from one place

If for whatever reason you would rather use your in-house screening tools, you can still get all the benefits of our curated database. The contents of our complete database are available in a single SDF file from a memorable address. You can freely download it, work with it locally and come back to our Find (Multiple) Chemicals page to buy your best hits.

Creating collections by drawing

We mentioned this feature in our previous post but it is worth repeating here: we've expanded the New Collection button with the ability to directly upload your SDF file or start off the created collection by drawing in a molecule first. 

New tutorial videos

Do you want to know more about how our Find Chemicals, ChemAxon properties, 1-Click Scaffold Hop, 1-Click Docking and FTrees features work? We've prepared short, 5-10 minute videos that walk you through the whole process.

Revised quote form

We've moved around some fields, now ask for only the necessary information, but also added a field where you can enter a promo code. Incidentally, we are running a promotion until the 31st of March: if you enter mcule1storder when requesting a quote, you will get 15% off from your order — large or small — on mcule.com!

Easier 'search on this collection' action

On every collection you can now find a 'Search' button that sets up a new Workflow with your collection set as the input. This makes it easy, for example, to continue refining the results of a previous workflow.

Small tidbits
  • Made possible to download docking poses just like in 1-click docking since the download pdb option in the glmol viewer basically only works in chrome
  • Can't use a 'running' collection as input
  • We now send email about quote being processed (for registered users)
  • When there are so many collections that it requires scrolling when adding a molecule to a collection, if a new collection is created, the list now scrolls to the bottom.

Thursday, February 21, 2013

Growing Beyond 1-Click Docking

In this post, we'll show you how to go just one small step beyond our 1-Click Docking tool, and how this is actually a giant leap for your productivity.

If you're using our 1-Click Docking feature, you already know how simple and quick it is to get a first insight into about a ligand-target interaction and affinity: just draw in a ligand, select a target and push a button: within 60 seconds you are presented with your results. But what happens if you want to do a bit more than that, refine some parameters, dock more than one ligand in one go, customize the binding center or save your results permanently? You can do all this and more, although it might take two, or even three clicks (but not much more!), after a free signup.

The Workflow Builder follows the same flow as the 1-Click tools: there's an input, we do some processing and save it to an output. By default, the input is set to the Purchasable compounds collection, containing more than 4 million unique, purchasable compounds that have gone through our rigorous registration system, but you can also use your own collection of molecules, either by uploading an SDF file, or by drawing in a molecule, just as you did with the 1-Click tools:

The first benefit of using Workflow Builder is that since we're using a Collection as input, we can dock more than a single molecule after one another into the same target automatically.
The meat of a  "Two-Click" docking workflow contains a single Docking (Vina) filter, which is unsurprisingly similar to the 1-Click version, but with a few more parameters you can set:
As opposed to 1-Click Docking, where your results are ephemeral, a Workflow's results are themselves saved to a Collection, whose name we can specify:
And after pushing the Run button, we get our results, just as with 1-Click Docking. The difference is that these results are not only stored for your future reference, but can also be used as an input for your next workflow.

As a free registered user of mcule.com, you can dock 500 molecules each month for free. If you get the taste for docking, you can sign up for a 100k package.

Saturday, February 2, 2013

Introducing our new design

You might have noticed that mcule started looking a bit different (frankly, much better) in the last few days. To reflect the fact that we are no longer in beta, we've decided that our design needed to grow up as well. There are still some pieces that need to fall in place, and of course, we are continuously improving mcule, but we are excited to introduce the new site and show you some of the biggest improvements we've made.

The new Dashboard

When you are logged in, the first page you'll see from now on is the Dashboard. From here you'll be able to quickly access all areas of mcule: the 1-Click Applications, your recent Collections and search results as well as predefined Workflow templates you can use as jumping off points.

Restructured navigation

We've given more descriptive names to our Search and Screen features. From now on, you will be able to make simple Exact, Similarity and Substructure searches on the Find Chemicals page. The Workflow Builder is the new, more descriptive name for what was previously somewhat opaquely called Screen. We've moved their links around on the top navigation bar as well.

Pre-defined Workflows

We've added three workflow templates that are accessible from the Dashboard to help you get started using the Workflow Builder. Each template is usable by itself, but really, they are meant to show you how you can use our filters to achieve various tasks. Feel free to experiment!

Workflows now flow

We’ve split the form we’ve used previously into two, so it’s easier to see what the input and output is in the Workflow Builder. Sounds like a minor change, but we think it greatly clarifies how to better use this feature. For example, did you know that you can use any previous workflow's result as the input for the next one? T

Simplified input

If you just want to paste an InChI or a SMILES, why waste your time fiddling with the sketcher? Or, if you’d like to draw in your molecule, why would you need any other fields? Input is now quicker and easier, not to mention less confusing.

All the small things

Fixing the bug that's been bothering us for days or adding a small button to a page in just the right place is unlikely to make the headlines, but nevertheless they are important. Who knows, maybe you bumped into one of them and you'll be glad to know that it's fixed, or that it's there. We've collected some of the smaller but no less important changes we've made:

  • You can upload molecules directly when creating a new collection
  • When viewing a docking pose, the view is rotated around the docked ligand
  • When viewing a docking pose, the docking target's name brings you directly to the target's index page
  • Fixed issues with unnecessarily added or missing bonds in GLmol
  • In the Docking (Vina) filter, you can now specify a binding center by clicking on an atom in the viewer
  • Uploading a .sdf.gz no longer gives an error
  • You are now notified if you are over your limits before you submit a new screen job
  • You are now warned if you add the same property twice in the property filter
  • and various other fixes and improvements on the backend