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May2024 - new files for the IQB workshop (#32)
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* eliminated one variable in the final cell

* added an exercise for the workshop and homework

* starting a notebook on small molecules

* first draft of the search for trypsin ligands

* second image for the EC_class_ligands_search notebook

* first image for the EC_class_ligands_search notebook

* latest update with Jessica's suggested changes

* a ligand file for the EC_Class notebook

* images for the new notebooks

* first attempt at ligand modification

* optimize in 3D and print 3D sdf files

* ligand 13U and 3 modified ligands in 3D

* Exploring AllChem MMFF

* changed the ligand to be used in the rdkit notebook

* fully functional notebook with glucose and ATP test cases

* restarted notebooks and cleared all outputs

* restarted and cleared all output

* Adds notebook to TOC, adds missing image

---------

Co-authored-by: Jessica Nash <[email protected]>
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@paulcraig @janash
paulcraig and janash committed Jun 10, 2024
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1 change: 1 addition & 0 deletions biochemist-python/_toc.yml
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Expand Up @@ -13,3 +13,4 @@ chapters:
- file: chapters/biopython_mmcif
- file: chapters/rcsb_api
- file: chapters/MolVis_with_iCN3D
- file: chapters/EC_class_ligands_search
357 changes: 357 additions & 0 deletions biochemist-python/chapters/EC_class_ligands_search.ipynb
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1,663 changes: 1,663 additions & 0 deletions biochemist-python/chapters/Modifying_Ligands_with_rdkit.ipynb
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70 changes: 70 additions & 0 deletions biochemist-python/chapters/SmallMolVis.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "739f4a0d-a082-417a-a983-225798383b06",
"metadata": {},
"source": [
"# Viewing Small Molecules in iCN3D\n",
"\n",
"While most people use iCN3D to view proteins and other macromolecular structures, it can also be used to explore small molecules of interest. The simplest way to do this is to find the small molecule on [PubChem](https://pubchem.ncbi.nlm.nih.gov/), capture its unique identifier and modify the iCN3D code we have used so far, replacing `mmdbid` or `pdbid` with `cid`.\n",
"\n",
"Here is the [PubChem Search Page for ATP](https://pubchem.ncbi.nlm.nih.gov/) page which contains 231 compounds. \n",
"![ATP Search Results](images/PubChem_ATP_231.png \"ATP Search Results\")\n",
"\n",
"Explore the page to find the line that says, **Compound CID: 644208**. The number **644208** is the critical piece of information. If PubChem contains a 3D version of this molecule, you can view it in iCN3D.\n"
]
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138 changes: 138 additions & 0 deletions biochemist-python/chapters/data/ligand13U-3D.sdf
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156 changes: 156 additions & 0 deletions biochemist-python/chapters/data/ligand13Uipr-3D.sdf
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