Showing posts with label vendor. Show all posts
Showing posts with label vendor. Show all posts

10 December 2018

Poll results: library vendors

Our latest poll has just closed, and the results are quite interesting. We asked three questions:

1) Have you bought fragments in the past few years?
2) Which of the following vendors would you RECOMMEND?
3) Which of the following vendors would you AVOID?

First, a paragraph on methodology. The poll ran from November 3 through December 7. Due to the limitations of the free version of Crowdsignal (formerly Polldaddy), I have no way of knowing how many individuals responded to questions 2 or 3 (respondents could choose multiple answers). This was the purpose of question 1; 37 people answered yes, and 12 people answered no. Assuming that only people who answered yes answered questions 2 and 3, I divided the responses to questions 2 and 3 by 37 to give percentages. So for example, 33 people would recommend Enamine, which is 89%. If some people who answered no to question 1 answered 2 and/or 3, or answered questions 2 and/or 3 but not 1, the percentages may be overestimates. This seems possible, as the total number of people who would recommend or avoid Enamine adds up to 36. So either nearly everyone who said they bought fragments did so from Enamine, or more people responded than were accounted for by answering “yes” to whether they purchased fragments.

The results are shown here.


The first thing that jumps out is the popularity of Enamine – which is recommended by nearly 90% of respondents. Life Chemicals, Maybridge, ChemBridge, and Key Organics are each recommended by more than 30%, while Vitas-M, ChemDiv, and Asinex are each recommended by 16-24% of respondents. Seven other vendors were recommended by 2 or fewer respondents.

The second observation is that, for the most part, people seem fairly happy with their vendors: each named vendor would be avoided by fewer than 10% of respondents. That said, the relative numbers vary considerably: only one respondent would avoid Life Chemicals, while 18 would recommend them. In contrast, for some of the less popular suppliers, the number of people who would avoid them was comparable to the number who would recommend them.

Finally, I was pleased to see that although a few respondents selected “other” for vendors they would recommend, these were outnumbered by the number selecting “others” they would avoid. That suggests the list provided in the poll captured most trusted vendors. That said, there is no way of knowing whether, for example, the 7 respondents who chose to recommend “other” vendors all had the same vendor in mind, or up to 7 different ones.

Of course there are caveats (and more in the methodology section above). First, the response rate is lower than most of our other polls, reflecting the fact that library generation is not something done lightly or frequently. Second, the first question was deliberately vague; people may have different definitions of “past few years,” and some vendors may have improved or deteriorated. Third, we have no way of knowing how many organizations are represented; if many people responded from a single company this could bias the results. Fourth, we are dependent on the honesty of respondents – we don’t know whether vendors recommended themselves.

Finally, please leave comments, positive or negative, especially if you would recommend vendors not included in the poll. Remember, you can comment anonymously.

04 November 2018

Library vendor poll!

A good fragment library is essential for generating good fragment hits. Earlier this year we asked about fragment size and library size, and summarized the results here.

Some folks make their own fragments, but this is expensive, and it’s probably fair to say that most fragment libraries contain a large fraction of commercially available compounds. Unfortunately, what you buy is not always what you get: sometimes the wrong compound is sent, or the compound is not as pure as advertised. As this post makes clear, different vendors have different track records.

Two years ago we highlighted a number of fragment library vendors. The current poll first asks whether you’ve bought fragments in the past several years. (Please answer this question as otherwise I have no idea how many people actually vote.)

If the answer to the first question is yes, the second question asks which vendors you would recommend buying from – presumably because you’ve had good experiences with them in the past few years. You can vote for as many as you’d like.

Finally, the third question asks which vendors you would avoid.

Please vote on the right-hand side of the page, and feel free to leave comments below, particularly if you've used vendors not on the list.

And on the subject of voting, if you are eligible to vote in the United States, please make sure to do so before the polls close on November 6.

Democracy atrophies when citizens don’t exercise their rights.

01 June 2016

Fragment library vendors - 2016 version

It's been two years since we last updated our list of commercial fragment libraries, and there have been several changes. The prompt for updating the list is a new Perspective published in J. Med. Chem. by György M. Keserű & György G. Ferenczy (Hungarian Academy of Sciences), Mike Hann & Stephen Pickett (GlaxoSmithKline), Chris Murray (Astex), and me. This covers all aspects of fragment library design, so definitely check it out.

One table in the Perspective compares various libraries, both commercial and proprietary. One of the manuscript reviewers asked if we could evaluate the various vendors, particularly given some negative experiences with commercial compounds. Such direct criticism (and praise!) can be awkward in the peer-reviewed literature, but is more acceptable in an online forum - think of Yelp for library suppliers. Please comment (anonymously if desired) if you've had experiences, positive or negative, with these vendors, and please feel free to add any we omitted.

Note that this list only includes companies that sell their libraries (as opposed to just using them internally).

ACB Blocks: 1280 compounds, 19F NMR-oriented, RO3 compliant, predicted to be soluble, purity >96%

Analyticon: 213 compounds, fragments from nature, RO3 compliant, high solubility, purity >95%

Asinex: >22,000 compounds

ChemBridge: >7000 compounds, RO3 compliant with predicted solubility; minimum purity 90% by 1H NMR

ChemDiv: >4000 3D fragments

Enamine: Multiple subsets including >18,000 RO3 compliant, ~1800 "Golden", and >126,000 with < 20 heavy atoms. Also separate fluorinated, brominated, sp3-rich, and covalent subsets.

InFarmatik: 1700 member consolidated library with different subsets (3D, GPCR, kinase)

IOTA: 1500 diverse, mainly RO3 compliant fragments

Integrex: 1500 compounds with diversity in shape and chemical structure, RO3 allowing one violation

Key Organics: ~26,000 compounds total with multiple subsets including 1166 with assured solubility and RO3 compliant as well as brominated, fluorinated, and CNS-directed fragments

Life Chemicals: 31,000 fragments of which 14,000 are RO3 compliant; also fluorinated, brominated, covalent, Fsp3-enriched, and covalent subsets

Maybridge: >30,000 fragments in total. The 2500 Diversity collection is guranteed soluble at 200 mM in DMSO and 1 mM in PBS.  NMR spectra are available (in organic solvent). It is available in many formats, from powder to DMSO-d6 solution. A smaller 1000-fragment subset is also available.

Otava: >12,000 fragments with various subsets including fluorinated, brominated, and metal-chelating

Prestwick: 910 mainly derived from drugs, RO3 compliant

Timtec: 3200 compounds, structurally diverse with predicted high solubility

Vitas-M: ~19,000 fragments, RO3 compliant

Zenobia:  968 fragments from different design paradigms, cores from drugs, higher Fsp3, flexible cores

19 May 2014

Fragment Library Vendors (2014 Edition)

We have been updating a lot of lists recently.  One that I think has changed significantly, is the fragment library vendor list, last updated in 2010. As Dan said four years ago, FOB Chris Swain has done a great job of curating who is selling what.  Instead of duplicating efforts, I will just focus on what has changed and making some comments.  I am not going to list companies that have libraries you can access, only those that sell outright their libraries. 

What are the keys for purchasing a good library?  I think minimally, purity and aqueous solubility should be experimentally tested and guaranteed.  I note those vendors who specifically point this out, but one should not assume that those who don't also don't have this data.  Comments can be sent directly to me or made below, and I will update this list.

Some general thoughts: 
  • There is no special sauce.  Every library is good and will work for you. It's the choice of screen and how you prosecute it after that makes the difference.
  • You don't need no stinkin' IP. 

3DFrag Consortium (New 2014):  I think this ran its course.  While I think by and large it had great ideas I don't think it ever truly answered the question "Do 3D fragments work better (in some areas)?"

Analyticon (New 2014): This is another example of fragments from nature.  The utility of these types of libraries are still up for discussion

Asinex: "Inspired by Nature" is its tagline.  However, they do have focused libraries, for such targets as PPIs.  They have 3159 in this library.. 

Chembridge: The collection is now 7000+ compounds (was 5000).  The guarantee greater than 90% purity, but nothing about solubility. 

Chemdiv (New 2014): Their collection is almost 14,000 fragments.

Enamine: More than doubled in size, from 12,000 to more than 28,000. 

Iota: I think they were the first to regularly use nPMI in their compound assesment.  You can only look at their library under CDA. 

Key Organics: They have quite a few specialized fragment libraries: CNS, self-assembly, brominated, fluorinated, and chiral cyclic molecules, in addition to their main libraries.  They guarantee 95% purity, 1mM aqueous solubility, solubility up to 200 mM in DMSO, and with almost no overlap with the Maybridge collections (68 compounds).

Life Chemicals:They are now up to 47,500 fragment molecules (less than 300 MW), of course only 31,000 of these exist, the other 16,000 can be made upon request.  They have 3900 19F fragments.  In terms of those that have experimental solubility, there are 8200.  However, 75% are soluble at 1mM, and 60% at 5mM in PBS.   So, always read the fine print.  They are also the vendor for the Zen-Life library, another library based on nature. 

Maybridge: The grandfather of them all.  30,000 fragments in total.  The 2500 Diversity collection is guranteed soluble at 200 mM in DMSO and 1mM in PBS.  The NMR spectrum is available, but only in organic solvent. It is available in many formats, from powder to DMSO-d6 solution. 

Otava: 8800 fragments in general.  800 19F fragments.  And 575 chelating fragments, if you want a warhead and all the issues they bring with.

Prestwick: 2200 fragments.

Timtec: No number available, but also can be shipped in DMSO solution. 

Vitas-M: The least helpful website out there.  It's Voldemort Rule compliant and available in multiple formats: mg, mcmol, sets, DMSO solution, dry film.

Zenobia:  Several different collections of very small fragments.