Added 1AKI DOI

bioexcel · Feb 27, 2024 · 554dc86 · 554dc86
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diff --git a/biobb_wf_md_setup/docs/source/tutorial.md b/biobb_wf_md_setup/docs/source/tutorial.md
@@ -1,7 +1,7 @@
 # Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
 **Based on the official GROMACS tutorial:** [http://www.mdtutorials.com/gmx/lysozyme/index.html](http://www.mdtutorials.com/gmx/lysozyme/index.html)
 ***
-This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI). 
+This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb)). 
 ***
 
 ## Settings
@@ -56,7 +56,7 @@ jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
 <a id="input"></a>
 ## Input parameters
 **Input parameters** needed:
- - **pdbCode**: PDB code of the protein structure (e.g. 1AKI)
+ - **pdbCode**: PDB code of the protein structure (e.g. 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb))
 
 
 ```python

diff --git a/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html b/biobb_wf_md_setup/html/biobb_MDsetup_tutorial.web.html
@@ -13079,7 +13079,7 @@
 <div class="text_cell_render border-box-sizing rendered_html">
 <h1 id="Protein-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">Protein MD Setup tutorial using BioExcel Building Blocks (biobb)<a class="anchor-link" href="#Protein-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">&#182;</a></h1><p><strong>Based on the official GROMACS tutorial:</strong> <a href="http://www.mdtutorials.com/gmx/lysozyme/index.html">http://www.mdtutorials.com/gmx/lysozyme/index.html</a></p>
 <hr>
-<p>This tutorial aims to illustrate the process of <strong>setting up a simulation system</strong> containing a <strong>protein</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>Lysozyme</strong> protein (PDB code 1AKI).</p>
+<p>This tutorial aims to illustrate the process of <strong>setting up a simulation system</strong> containing a <strong>protein</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>Lysozyme</strong> protein (PDB code 1AKI, <a href="https://doi.org/10.2210/pdb1AKI/pdb">https://doi.org/10.2210/pdb1AKI/pdb</a>).</p>
 <hr>
 <h2 id="Settings">Settings<a class="anchor-link" href="#Settings">&#182;</a></h2><h3 id="Biobb-modules-used">Biobb modules used<a class="anchor-link" href="#Biobb-modules-used">&#182;</a></h3><ul>
 <li><a href="https://github.com/bioexcel/biobb_io">biobb_io</a>: Tools to fetch biomolecular data from public databases.</li>
@@ -13132,7 +13132,7 @@ <h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-ste
 <p><a id="input"></a></p>
 <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-parameters">&#182;</a></h2><p><strong>Input parameters</strong> needed:</p>
 <ul>
-<li><strong>pdbCode</strong>: PDB code of the protein structure (e.g. 1AKI)</li>
+<li><strong>pdbCode</strong>: PDB code of the protein structure (e.g. 1AKI, <a href="https://doi.org/10.2210/pdb1AKI/pdb">https://doi.org/10.2210/pdb1AKI/pdb</a>)</li>
 </ul>
 
 </div>

diff --git a/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb b/biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
@@ -7,7 +7,7 @@
     "# Protein MD Setup tutorial using BioExcel Building Blocks (biobb)\n",
     "**Based on the official GROMACS tutorial:** [http://www.mdtutorials.com/gmx/lysozyme/index.html](http://www.mdtutorials.com/gmx/lysozyme/index.html)\n",
     "***\n",
-    "This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI). \n",
+    "This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Lysozyme** protein (PDB code 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb)). \n",
     "***\n",
     "\n",
     "## Settings\n",
@@ -66,7 +66,7 @@
     "<a id=\"input\"></a>\n",
     "## Input parameters\n",
     "**Input parameters** needed:\n",
-    " - **pdbCode**: PDB code of the protein structure (e.g. 1AKI)"
+    " - **pdbCode**: PDB code of the protein structure (e.g. 1AKI, [https://doi.org/10.2210/pdb1AKI/pdb](https://doi.org/10.2210/pdb1AKI/pdb))"
    ]
   },
   {