NeBULA
(Next-Generation Bioisostere Utility Libraries)
[Paper]
A web-based novel drug design platform for up-to-date bioisosteric replacement
🔗 Online tool: http://nebula.alphamol.com.cn:5001/
<h2>Requirements</h2>
<pre><code>conda create -n nebula python=3.9
pip install rdkit==2022.3.5 pandas numpy==1.22.4</code></pre>
<p>Note: you can use -- pip install "numpy<2.0" -- for more compatible version</p>
<h2>Folder format</h2>
<pre><code>--nebula
--reaction.py
--Reaction_Fsp3-rich.csv
--README.md</code></pre>
<h2>How to use</h2>
<pre><code>
conda activate nebula
cd nebula
</code></pre>
<p>Note: you can use -- unzip Reaction_Fsp3-rich.zip -- to unzip necessary file</p>
<h3>1. Pass the parameter (in non-interactive mode)</h3>
<p>Filename <em>reaction.py</em>, which can be called in the terminal like this:</p>
<pre><code>python reaction.py --smiles "c1(c(COc2nc([C@H]3CC[N@@H+](Cc4nc5ccc(C(=O)[O-])cc5n4C[C@@H]4CCO4)CC3)ccc2)ccc(C#N)c1)F"</code></pre>
<p>"c1(c(COc2nc([C@H]3CC[N@@H+](Cc4nc5ccc(C(=O)[O-])cc5n4C[C@@H]4CCO4)CC3)ccc2)ccc(C#N)c1)F" means the SMILES you want to replace.</p>
<h3>2. Without passing parameters (interactive mode)</h3>
<p>If executed directly in the terminal,</p>
<pre><code>python reaction.py</code></pre>
<p>the program prompts for input:</p>
<pre><code>Enter SMILES:</code></pre>
<p>Input the appropriate content and press Enter to execute, the program will be based on the input to generate a "current time folder" contains: </p>
<pre><code>--%Y%m%d_%H%M%S
--reaction_products.csv</code></pre>
<h3>3. Bioisosteric replacement for batch input</h3>
<pre><code>python reaction.py --input_csv molecules.csv</code></pre>
<p>You need to make sure the <em>molecules.csv</em> file has SMILES header </p>
Reference
- Huang, S., Wang, S., Dong, J., Xu, M., & Yuan, S. (2025). NeBULA: a web-based novel drug design platform for up-to-date bioisosteric replacement. Medicine in Drug Discovery, 28, 100231.
https://doi.org/10.1016/j.medidd.2025.100231
