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‎education/HADDOCK3/HADDOCK3-antibody-antigen/index.md‎

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In case of a workshop of course, HADDOCK3 will usually have been installed on the system you will be using.
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In case HADDOCK3 is not pre-installed in your system you will have to install it.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
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‎education/HADDOCK3/HADDOCK3-nanobody-antigen/index.md‎

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Another important feature of these molecules is that the highly conserved amino acids that are not part of the CDRs, namely the **framework regions (FRs)**,
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can play a role in the binding to the antigen.
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Predicting the structure of a nanobody-antigen complex is very challenging, as the epitope can be located in any part of the antigen molecule. In the last years AlphaFold2-Multimer has been shown to be able to predict the correct structure of the nanobody-antigen complex for a limited number of cases. This is due to the fact that there's no co-evolution between the antibody and antigen sequences, which makes the prediction of the correct conformation extremely difficult. AlphaFold3 is expected to improve the prediction of the nanobody-antigen complex, but still fails for many cases.
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Predicting the structure of a nanobody-antigen complex is very challenging, as the epitope can be located in any part of the antigen molecule. In the last years AlphaFold2-Multimer has been shown to be able to predict the correct structure of the nanobody-antigen complex for a limited number of cases. This is due to the fact that there is no co-evolution between the antibody and antigen sequences, which makes the prediction of the correct conformation extremely difficult. AlphaFold3 is expected to improve the prediction of the nanobody-antigen complex, but still fails for many cases.
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This tutorial demonstrates the use of the new modular HADDOCK3 version for predicting
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the structure of a nanobody-antigen complex using different possible information scenarios, ranging
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We assume that you have a working installation of HADDOCK3 on your system.
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In case HADDOCK3 is not pre-installed in your system you will have to install it.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
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‎education/HADDOCK3/HADDOCK3-protein-DNA-basic/index.md‎

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We assume that you have a working installation of HADDOCK3 on your system.
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In case HADDOCK3 is not pre-installed in your system you will have to install it.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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In this tutorial we will use the PyMOL molecular visualisation system. If not already installed, download and install PyMOL from [here](https://pymol.org/){:target="_blank"}. You can use your favourite visualisation software instead, but be aware that instructions in this tutorial are provided only for PyMOL.
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‎education/HADDOCK3/HADDOCK3-protein-glycan/index.md‎

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We assume that you have a working installation of HADDOCK3 on your system.
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In case HADDOCK3 is not pre-installed in your system you will have to install it.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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To obtain HADDOCK3, fill the [registration form](https://docs.google.com/forms/d/e/1FAIpQLScDcd0rWtuzJ_4nftkDAHoLVwr1IAVwNJGhbaZdTYZ4vWu25w/viewform?){:target="_blank"}, navigate to [its repository][haddock-repo]{:target="_blank"}, and then follow the [installation instructions](https://www.bonvinlab.org/haddock3-user-manual/install.html){:target="_blank"}.
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Further we are providing pre-processed PDB files for docking and analysis (but the
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preprocessing of those files will also be explained in this tutorial).

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