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retrosyntheis tools [message #1407] Wed, 22 September 2021 11:48 Go to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
Junior Member
hi all,
Please any one can point me to retrosynyesis tools we can use from data warrior?
your help is much appreciated
Re: retrosyntheis tools [message #1416 is a reply to message #1407] Thu, 23 September 2021 21:10 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 211
Registered: June 2019
Senior Member
If your organization supports an account on spaya.ai, then a right-click on the structure of interest offers access to suggestions. You have 30 days to venture out and get familiar enough with this service to come to a decision to purchase their service, or not.

They are not the only ones in the field to predict reactions/to offer retrosynthesis (e.g, https://rxn.res.ibm.com/, or https://askcos.mit.edu/retro/); you may enter the targeted structure by the SMILES string DataWarrior can assign to the molecule structures. If you have access to and some familiarity with Python, AiZynthFinder by the Reymond group may be an interesting example (open source code, permissive MIT licence), too.

[1a] Genheden, S., Thakkar, A., Chadimová, V. et al. AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J Cheminform 12, 70 (2020) (https://doi.org/10.1186/s13321-020-00472-1)
[1b] Retrosynthetic accessibility score (RAscore) – rapid machine learned synthesizability classification from AI driven retrosynthetic planning, Thakkar et al. Chem. Sci., 2021,12, 3339-3349 (https://doi.org/10.1039/D0SC05401A)
Re: retrosyntheis tools [message #1419 is a reply to message #1416] Fri, 24 September 2021 16:15 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Thank you, very helpful
Re: retrosyntheis tools [message #1420 is a reply to message #1419] Fri, 24 September 2021 16:44 Go to previous messageGo to next message
Paul Smith is currently offline  Paul Smith
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Registered: September 2021
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To add on what has been said on Spaya retrosynthesis tool, they organize some webinars that can be very useful to attend: there is one on September 28th. Video recordings are also available on Youtube.

In a nutshell, I can recommend Spaya which is a reliable, easy to use, and comprehensive tool and where you can select building blocks providers of interest for a given compound price.

[Updated on: Fri, 24 September 2021 17:22]

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Re: retrosyntheis tools [message #1421 is a reply to message #1420] Fri, 24 September 2021 18:02 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Thank you for the heads up, I will try yo register to their webinar on 28th.
Re: retrosyntheis tools [message #1484 is a reply to message #1421] Wed, 26 January 2022 11:57 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Hi All,
Any one can point me to relevant retrosyntheis articles?
Thanks in advance
Re: retrosyntheis tools [message #1485 is a reply to message #1484] Wed, 26 January 2022 12:03 Go to previous messageGo to next message
Drobert is currently offline  Drobert
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Hi,
here is the link to the latest ChemRxiv about Spaya.
I have found it very interesting to be honest.
Have a good reading!
Re: retrosyntheis tools [message #1486 is a reply to message #1484] Thu, 27 January 2022 07:54 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
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Your question does not clarify if your interest is about the classical rules, or about contemporary implementation of retrosynthethic algorithms into computer programs. For the former (humanoid recognition of pattern, disconnection into known precursors) E. J. Corey was one prominent author who formalized the approaches.[1, 2] But there are plenty publications about the later as well[3,4,5] and a listing here is opinionated and incomplete. You may use the references below to expand the bibliographic search further.

Norwid

[1] Corey, Nobel lecture in Angewandte 1991, 30, 455-465; https://doi.org/10.1002/anie.199104553.
[2] E. J. Corey, X-M. Cheng (1995). The Logic of Chemical Synthesis. New York: Wiley. ISBN 978-0-471-11594-6.
[3] Szymkuć S. et al. Computer-Assisted Synthetic Planning: The End of the Beginning. Angewandte 2016, 55, 5904-5937; https://doi.org/10.1002/anie.201506101
[4] Badowski, T. et al. Synergy Between Expert and Machine-Learning Approaches Allows for Improved Retrosynthetic Planning. Angewandte 2019, 55, 725-730; https://doi.org/10.1002/anie.201912083
[5] Thakkar, A. et al. Retrosynthetic accessibility score (RAscore) – rapid machine learned synthesizability classification from AI driven retrosynthetic planning. Chem. Sci. 2021, 12, 3339-3349; https://doi.org/10.1039/D0SC05401A.
Re: retrosyntheis tools [message #1488 is a reply to message #1486] Mon, 31 January 2022 17:19 Go to previous messageGo to next message
Drobert is currently offline  Drobert
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To add to this topic, I have recently read the ChemRxiv paper on Spaya:
Integrating Synthetic Accessibility with AI-based Generative Drug Design - https://chemrxiv.org/engage/chemrxiv/article-details/61c19ee 67f367e034f5adb11

In a general way, I have found Spaya software very fast, robust and informative for my research. You can also access a free trial version of it by registering on their website - https://spaya.ai/.

[Updated on: Tue, 01 February 2022 10:47]

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Re: retrosyntheis tools [message #1492 is a reply to message #1488] Tue, 01 February 2022 16:15 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
Junior Member
Drobrt,
Thank you, will read the article and get back.
Sound very intersting
Scott
Re: retrosyntheis tools [message #1493 is a reply to message #1486] Tue, 01 February 2022 16:33 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Thank you Norwid, very helpful
Re: retrosyntheis tools [message #1519 is a reply to message #1493] Wed, 23 February 2022 11:48 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
Junior Member
Hi, I recently tried chiral pool functionality in Spaya. It seems like a good function. Any one else has tried it?
Re: retrosyntheis tools [message #1520 is a reply to message #1519] Wed, 23 February 2022 11:50 Go to previous messageGo to next message
Drobert is currently offline  Drobert
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Hi Scott, I have tried it and it definitely works well.
Re: retrosyntheis tools [message #1521 is a reply to message #1520] Wed, 23 February 2022 11:51 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Good to hear your thoughts Drobert
Re: retrosyntheis tools [message #1563 is a reply to message #1521] Wed, 23 March 2022 11:39 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
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Registered: September 2021
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Hi All,
I wonder if there are any up coming training/webinar sessions for retrosyntheis.
Re: retrosyntheis tools [message #1564 is a reply to message #1563] Wed, 23 March 2022 12:13 Go to previous messageGo to next message
Drobert is currently offline  Drobert
Messages: 4
Registered: January 2022
Junior Member
Hi,

There are these upcoming webinars that you might be interested in attending:

Spaya: AI-driven accurate synthetic accessibility - from ‘precise analysis to massive scoring’ on March 29th, 2022 at 10am CEST and 5pm CEST.

Registration link for 10am CEST session:
https://us06web.zoom.us/webinar/register/9716470199061/WN_OP 3Ax_6zQ-GDddfeQfgxxA

Registration link for 5pm CEST session: https://us06web.zoom.us/webinar/register/1516470198529/WN_ao isMzAzR5OnOjVSmXnsIA

Best,
Robert
Re: retrosyntheis tools [message #1566 is a reply to message #1564] Wed, 23 March 2022 12:49 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
Messages: 11
Registered: September 2021
Junior Member
Hi All,
I wonder if there are any up coming training/webinar sessions for retrosyntheis.
Re: retrosyntheis tools [message #1567 is a reply to message #1563] Wed, 23 March 2022 12:50 Go to previous messageGo to next message
scottwabc01 is currently offline  scottwabc01
Messages: 11
Registered: September 2021
Junior Member
Thank you Robert
Re: retrosyntheis tools [message #1568 is a reply to message #1567] Thu, 24 March 2022 08:57 Go to previous message
nbehrnd is currently offline  nbehrnd
Messages: 211
Registered: June 2019
Senior Member
For the interested reading this thread a bit later, by today, a brief (i.e., non-exhaustive) search on youtube yields three webinars potentially relevant to and about Spaya in particular. In chronological order of the recording:

+ AI for Retrosynthesis Spaya webinar; by June 10th, 2020 [1]
+ Retrosynthesis in the AI era: opportunities and pitfalls; by September 23, 2020 [2]
+ AI Enhanced Retrosynthesis webinar: Spaya for Chemists; by March 30th, 2021 [3]

Norwid

[1] https://www.youtube.com/watch?v=M7vH9xMdLgw
[2] https://www.youtube.com/watch?v=I2cdBHaWDxE
[3] https://www.youtube.com/watch?v=mPaGnc_kfww
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