Chem: MMP: Updated documentation #3254
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| * [Substructure search](#substructure-search--filtering). | |||
| * [Chemical space analysis](#chemical-space). | |||
| * Structure analysis using [R-groups decomposition](#r-groups-analysis), [scaffold tree](#scaffold-tree-analysis), [elemental analysis](#elemental-analysis). | |||
| * SAR: [activity cliffs](#structure-relationship-analysis), [matched molecular pairs](#matched-molecular-pairs). | |||
| * SAR: [activity cliffs](#structure-relationship-analysis), [matched molecular pairs](./matched-molecular-pairs.md). | |||
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Please use the Markdown-style links in wiki. Links like this ^ create issues in Docusaurus
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You can't just delete a section from the Level 1 page (Cheminformatics) and move it to a separate document. You need to keep a section with the short overview and GIF, and link to a separate document instead. Please update
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Moved MMP article back to chem.md file
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| # Matched molecular pairs | |||
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We don't use Level 1 headers in Docusaurus. Instead, we add the "title" front matter, which Docusaurus uses to automatically generate the Title. Please see the guide at https://datagrok.ai/help/develop/help-pages/markdown#table-of-contents-headers
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You also need to add front matter for keywords and description
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Fixed - using H3 headers as for other articles within chem.md.
| well-defined molecular modifications and quantify their impact on key properties such | ||
| as potency, solubility, permeability, and/or ADMET characteristics. | ||
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| MMP analysis is particularly valuable in lead optimization, where systematic exploration of chemical space can guide the design of more effective drug candidates. |
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Simplify. Paragraph 1 and 2 should be combined into one. Cut unnecessary words like "particularly": "particularly valuable in" --> "used in ... "
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Agree, this should be shorter with more substance. For instance this is how ChatGPT suggests to simplify the first two sentences:
The Matched Molecular Pairs (MMP) tool helps analyze small structural changes in chemical datasets and their effects on properties like potency, solubility, permeability, and ADMET.
| as potency, solubility, permeability, and/or ADMET characteristics. | ||
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| MMP analysis is particularly valuable in lead optimization, where systematic exploration of chemical space can guide the design of more effective drug candidates. | ||
| By studying how molecular fragments influence activity, the tool helps users make data-driven decisions when selecting modifications to improve lead compounds. |
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This paragraph repeats the ideas in the first two. Cut/combine
| MMP analysis is particularly valuable in lead optimization, where systematic exploration of chemical space can guide the design of more effective drug candidates. | ||
| By studying how molecular fragments influence activity, the tool helps users make data-driven decisions when selecting modifications to improve lead compounds. | ||
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| Traditionally, lead optimization relies on trial and error, guided by medicinal chemistry intuition. |
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This is not an explanatory article. We don't need to provide background. There's no value for the users.
| * **The upper table (Fragments)** shows all fragment substitutions found in the dataset. It includes the frequency of each substitution and the | ||
| corresponding change in the analyzed activity or property. There are two modes to explore fragments dataset: | ||
| - *All* shows all found fragment pairs at once | ||
| - *Current* shows fragment pairs fount for current molecule in the initial dataset. |
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Fix spelling/grammar ("fount")
| Information message on the left top corner of the table shows how many rows of total are filtered. | ||
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| Click any row in the table to show all molecule pairs from the initial dataset having corresponding substitution. |
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Which table (top/bottom/grid?)
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How does it interact with grid? We should describe all interactions here (gird <>top table <> bottom table)
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Added some more details. Basically, there are two tables on the Substitutions tab. And we describe each table and available interactions for upper and lower table separately.
| * **The lower table (Molecule pairs)** shows all pairs of molecules associated with the | ||
| substitution from the upper table. It provides details about the analyzed | ||
| activity or property for each pair of molecules. | ||
| Click any row in the **Fragments** table to filter molecule pairs with current substitution. If *Current* mode is selected on **Fragments** table then pair containing current molecule from initial dataset will be on top. |
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Please run through grammarly - you have many grammar/spelling/punctuation mistakes in this how to section
| specified activity or property, with the arrow pointing toward the molecule with | ||
| the higher value. | ||
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| * **Molecule pairs** table. The same as on **Substitutions** tab. Show or hide the table using **Show Pairs** checkbox above the scatter plot. |
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Our convention is to use "scatterplot", not "scatter plot". In any case, whichever way you choose, it should be consistent. You do it both ways (line 116 and line 122)
| properties. | ||
| * Whether new molecule already exists in the initial dataset or newly generated | ||
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| In the **Context panel** there is scatter plot showing observed vs predicted values for each activity for molecules from initial dataset. |
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Why is it here? It looks like the Context Panel applies only to the last tab?
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Actually, context panel is also available from other tabs. But for Generation tab it is specific and contains 'predicted vs observed' scatterplot
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