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I'm trying to perform a QSPR research and for it I need to generate a library of compounds. Now I'm using a plugin for MarvinSkectch for enumerating Markush structures but it doesn't work properly (maybe I misuse it). So I'm looking for a free/trial software that allows to generate compound library based on general structure.

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    $\begingroup$ Do you need to generate your own library? The ZINC library have millions of structures to download. $\endgroup$ – Camps Oct 16 '20 at 13:12
  • $\begingroup$ I plan to use to predict physico-chemical properties of particular classes of compounds, so I need to generate library from block that I will define myself. $\endgroup$ – roma ichenko Oct 16 '20 at 13:59
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    $\begingroup$ I already used LigBuilder, a de novo drug design software but I don't know if it is capable to generate molecules alone (it is designed to generate molecules interacting with a given target). $\endgroup$ – Camps Oct 16 '20 at 14:54
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    $\begingroup$ Take a look at this software: VLG or Virtual Library Generator is a tool for generating compounds by adding substituents to a scaffold, from here, I think it can do what you need. $\endgroup$ – Camps Oct 16 '20 at 19:35
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    $\begingroup$ Did Camps' suggestion of VLG help at all? $\endgroup$ – Tyberius Dec 3 '20 at 21:18
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Upon the request I'm sharing the solution I came to.

So, as I mentioned in the comments, I've finally make MarvinSkectch Markush enumeration feature to work properly. I don't really know what I've been doing wrong, as it just started working as intended. ChemAxon have a small tutorial on this feature. ChemAxon tutorial

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