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548 changes: 548 additions & 0 deletions education/HADDOCK24/HADDOCK24-protein-glycan/index.md

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3 changes: 3 additions & 0 deletions education/HADDOCK24/index.md
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Expand Up @@ -51,6 +51,9 @@ In this page you can find links to tutorials on the usage of our software and we
This tutorial demonstrate the modelling of protein-ligand complexes making use the shape-based modelling capabilities of HADDOCK.
It is an advanced tutorial requiring a Linux shell, which, next to using the HADDOCK2.4 webserver, also uses open-source chemoinformatics
toolkits such as [RDKit](https://www.rdkit.org/){:target="_blank"}.

* [**HADDOCK2.4 basic protein-glycan tutorial**](/education/HADDOCK24/HADDOCK24-protein-glycan):
This tutorial explains the modelling of protein-glycan complexes using the HADDOCK2.4 webserver and [PyMol](https://www.pymol.org){:target="_blank"} for visualisation/analysis. It is a basic, fully web-based tutorial requiring no Linux expertise.

* [**HADDOCK2.4 ligand binding site tutorial**](/education/HADDOCK24/HADDOCK24-binding-sites):
A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites.
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2 changes: 1 addition & 1 deletion education/HADDOCK3/HADDOCK3-protein-glycan/index.md
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## Defining restraints for docking


### Visualing the information about the bindind site
### Visualising the information about the binding site

Here we mimic a scenario where we have information about the glycan binding site on the protein, but no knowledge about which monosaccharide units are relevant for the binding. In this case (see Fig. 1), all the four beta-D-glucopyranose units are at the interface, although this might not be true in general, especially when longer glycans are considered.

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4 changes: 3 additions & 1 deletion publications/index.md
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---
## 2025

* M. Giulini#, V. Reys#, J.M.C. Teixeira, B. Jiménez-García, R.V. Honorato, A. Kravchenko, X. Xu, R. Versini, A. Engel, S. Verhoevenand **A.M.J.J. Bonvin**. [HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes](https://doi.org/10.1101/2025.04.30.651432). _BioRXiv._ 10.1101/2025.04.30.651432 (2025).
* A. Kryshtafovych, M. Milostan, M. Lensink, S. Velankar, **A.M.J.J. Bonvin**, J. Moult and K. Fidelis. [Updates to the CASP infrastructure in 2024](https://doi.org/10.22541/au.174646994.49522644/v1). _Authorea_ 10.22541/au.174646994.49522644/v1 (2025)

* M. Giulini#, V. Reys#, J.M.C. Teixeira, B. Jiménez-García, R.V. Honorato, A. Kravchenko, X. Xu, R. Versini, A. Engel, S. Verhoeven and **A.M.J.J. Bonvin**. [HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes](https://doi.org/10.1101/2025.04.30.651432). _BioRXiv._ 10.1101/2025.04.30.651432 (2025).

* M. Giulini#, X. Xu# and **A.M.J.J. Bonvin**. [Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles](https://doi.org/10.1101/2025.02.24.639865). _BioRXiv._ 10.1101/2025.02.24.639865 (2025).

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