adding protein folding content

docs/protein-folding/introduction-to-protein-folding.md

@@ -2,4 +2,7 @@
 title: Introduction to Protein Folding
 # sidebar_position: 2
 ---
-## Coming soon...
+
+:::note
+Coming soon!
+:::

docs/protein-folding/tools.md

@@ -1,4 +1,65 @@
 ---
 title: Tools
 sidebar_position: 2
----
+---
+
+Since the release of Alphafold there has been a variety of related models released for protein folding. We have gone through the literature and open source code repositories to provide a selection of tools that are ready for you to run on PLEX. 
+
+:::note
+All models we provide are research-grade software and are provided "as-is". We make use of existing, often academic, contributions. Please give credit to the creators of open-source work. **We are standing on the shoulder of giants.**
+:::
+
+:::info
+We have prepared a set of configurations for you that we list below. We are working on ways to have more control over individual parameters.
+:::
+
+
+## Mini: Colabfold
+[Colabfold](https://github.com/sokrypton/ColabFold) is an implementation of Alphafold that uses a multiple sequence alignment (MSA) Server, MMSeq2, instead of a local database to make using [Alphafold](https://github.com/deepmind/alphafold) more lightweight. The "mini" configuration runs a shallow MSA, performs one recycling and uses available templates to make a prediction. This is best used if you want to predict a protein structure very fast. 
+
+````
+./plex -app colabfold-mini -input-dir testdata/folding -gpu=true -network=true
+````
+
+:::note
+Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold: Making protein folding accessible to all.
+Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
+:::
+
+
+## Base: Colabfold
+The "base" configuration runs a shallow MSA, performs one recycling and uses available templates to make a prediction. It runs this prediction 5 times with different randomness seeds. This is best used if you want to predict a protein structure very fast and draw from a distribution of potential conformational substates. 
+
+````
+./plex -app colabfold-base -input-dir testdata/folding -gpu=true -network=true
+````
+
+:::note
+Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold: Making protein folding accessible to all.
+Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
+:::
+
+## Standard: Colabfold
+The "standard" configuration runs a full MSA, performs three recycling rounds and uses available templates to make a prediction. It runs this prediction 5 times with different randomness seeds. This is best used if you want to predict a state of the art structure and draw from a distribution of potential conformational substates.
+
+````
+./plex -app colabfold-standard -input-dir testdata/folding -gpu=true -network=true
+````
+
+:::note
+Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold: Making protein folding accessible to all.
+Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
+:::
+
+## Large: Colabfold
+The "large" configuration runs just like the standard configuration, but includes a GPU-accelerated relaxation step using Amber. It returns 25 predictions. This is best used when a lot of ressources are available and you want to predict a state of the art structure while drawing from a larger distribution of potential conformational substates.
+
+````
+./plex -app colabfold-large -input-dir testdata/folding -gpu=true -network=true
+````
+
+:::note
+Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. ColabFold: Making protein folding accessible to all.
+Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
+:::
+

docs/welcome/welcome.md

@@ -26,7 +26,7 @@ In these docs, you can find:
 - [Install PLEX here with 1 line of code.](/getting-started/install-plex)
 
 
-- Run a tool - check out our [Small Molecule Binding](../small-molecule-binding/overview) or [Protein Folding toolsets](../protein-folding/overview). For example, our small molecule binding toolset includes a workflow for docking small molecules & proteins, and for visualizing the results. **You can install PLEX, run an example model, and visualize the results in less than 5 mins!**
+- Run a tool - check out our [Small Molecule Binding](../small-molecule-binding/overview) or Protein Folding toolsets. For example, our small molecule binding toolset includes a workflow for docking small molecules & proteins, and for visualizing the results. **You can install PLEX, run an example model, and visualize the results in less than 5 mins!**
 
 - Find out more about our tools on our [website](https://labdao.xyz/tools).
 

sidebars.js

@@ -33,7 +33,7 @@ const sidebars = {
       label: 'Protein Folding',
       collapsed: true,
       items: [
-        'protein-folding/overview',
+        // 'protein-folding/overview',
         'protein-folding/tools',
         'protein-folding/run-an-example',
       ]