Skip to content

Commit

Permalink
replacing bianca links by wenmr
Browse files Browse the repository at this point in the history
  • Loading branch information
@amjjbonvin
amjjbonvin committed Jun 20, 2024
1 parent 8f4d5b1 commit aadc32a
Show file tree
Hide file tree
Showing 22 changed files with 93 additions and 93 deletions.
2 changes: 1 addition & 1 deletion education/HADDOCK/HADDOCK-CACA-guided/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -449,7 +449,7 @@ We can see that the CA-CA distance restraints (yellow dashes) are mostly at the
<hr>
## CA-CA distance restraint-driven docking with HADDOCK

__Note:__ _To perform CA-CA guided docking runs with HADDOCK, you will need to register as a user and request Expert or Guru level access. The registration page for HADDOCK can be found [here](https://bianca.science.uu.nl/auth/register/){:target="_blank"}._
__Note:__ _To perform CA-CA guided docking runs with HADDOCK, you will need to register as a user and request Expert or Guru level access. The registration page for HADDOCK can be found [here](https://wenmr.science.uu.nl/auth/register/){:target="_blank"}._


### Setting up the docking
Expand Down
4 changes: 2 additions & 2 deletions education/HADDOCK24/HADDOCK24-CASP-CAPRI-T70/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -118,14 +118,14 @@ You will see three directories and one file:

#### Registration / Login

In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://bianca.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://wenmr.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.

**Note:** The blue bars on the server can be folded/unfolded by clicking on the arrow on the left

#### Submission and validation of structures

We will launch two docking runs, one for the dimeric and one for the tetrameric form of this target.
For this we will make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) of the HADDOCK web server, where you will need to register as a user and request Expert or Guru level access [here](https://bianca.science.uu.nl/auth/register/).
For this we will make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) of the HADDOCK web server, where you will need to register as a user and request Expert or Guru level access [here](https://wenmr.science.uu.nl/auth/register/).

We will first set up a symmetrical tetramer docking run:

Expand Down
8 changes: 4 additions & 4 deletions education/HADDOCK24/HADDOCK24-Xlinks/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ Further, the required data to run this tutorial are the same as for the [DisVis
and should be downloaded from [**here**][link-data]{:target="_blank"}.
Once downloaded, make sure to unpack the archive.

Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://bianca.science.uu.nl/auth/register/haddock](https://bianca.science.uu.nl/auth/register/haddock).
Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock).

<hr>
## HADDOCK general concepts
Expand Down Expand Up @@ -377,7 +377,7 @@ cat restraints_filtered.txt | awk \'{if ( NF == 8 ) {print \"assi ( segid \",$1,

#### Registration / Login

In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://bianca.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://wenmr.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.

**Note:** The blue bars on the server can be folded/unfolded by clicking on the arrow on the left

Expand Down Expand Up @@ -483,7 +483,7 @@ job has successfully completed.

#### Registration and Submission

For this scenario we will make us of [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) after registering [here](https://bianca.science.uu.nl/auth/register/).
For this scenario we will make us of [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) after registering [here](https://wenmr.science.uu.nl/auth/register/).

* **Step 1:** Define a name for your docking run, e.g. *PRE5-PUP2-MS-interface*.

Expand Down Expand Up @@ -546,7 +546,7 @@ __Remember__ _to save the haddockparameter file for reference._

#### Registration and Submission

For this scenario we will make us of [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) after registering [here](https://bianca.science.uu.nl/auth/register/).
For this scenario we will make us of [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1) after registering [here](https://wenmr.science.uu.nl/auth/register/).

* **Step1:** Define a name for your docking run, e.g. *PRE5-PUP2-MS-crosslinks-interface*.

Expand Down
10 changes: 5 additions & 5 deletions education/HADDOCK24/HADDOCK24-antibody-antigen-basic/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ The small part of the Fab region that binds the antigen is called **paratope**.
In this tutorial we will be working with Interleukin-1β (IL-1β) (PDB code [4I1B](https://www.ebi.ac.uk/pdbe/entry/pdb/4i1b){:target="_blank"})) as an antigen and its highly specific monoclonal antibody gevokizumab (PDB code [4G6K](https://www.ebi.ac.uk/pdbe/entry/pdb/4g6k){:target="_blank"}) (PDB code of the complex [4G6M](https://www.ebi.ac.uk/pdbe/entry/pdb/4g6m){:target="_blank"}).


We will make use of the [HADDOCK2.4 webserver](https://bianca.science.uu.nl/haddock2.4){:target="_blank"}.
We will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}.

A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2){:target="_blank"} can be found in the following publications:

Expand Down Expand Up @@ -68,7 +68,7 @@ Throughout the tutorial, coloured text will be used to refer to questions or ins

In order to run this tutorial you will need to have the following software installed: [PyMOL][link-PyMOL].

Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://bianca.science.uu.nl/auth/register/haddock](https://bianca.science.uu.nl/auth/register/haddock){:target="_blank"}.
Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock){:target="_blank"}.

Further we are providing pre-processed PDB files for docking and analysis. They have been processed (see below) to facilitate their use in HADDOCK and for allowing comparison with the known reference structure of the complex. For this download and unzip the following [zip archive](input-data.zip) and note the location of the extracted PDB files in your system. You should find the following three files:

Expand Down Expand Up @@ -243,7 +243,7 @@ The answer to that question should be yes, but we can see some residues not colo

In previous steps we have identified the paratope and epitope residues of the antibody and antigen. Those can now be used to guide the docking. We will use this information to setup the docking.

If not provided with special workshop credentials, in order to start the submission you need first to register. For this go to [https://bianca.science.uu.nl/haddock2.4/](https://bianca.science.uu.nl/haddock2.4/){:target="_blank"} and click on **Register**.
If not provided with special workshop credentials, in order to start the submission you need first to register. For this go to [https://wenmr.science.uu.nl/haddock2.4/](https://wenmr.science.uu.nl/haddock2.4/){:target="_blank"} and click on **Register**.


To start the submission process, you are prompted for our login credentials. After successful validation of the credentials you can proceed to the structure upload under **Submit a new job**.
Expand All @@ -254,7 +254,7 @@ To start the submission process, you are prompted for our login credentials. Aft

### Submission and validation of structures

We will make us of the [HADDOCK 2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
We will make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.

In this stage of the submission process we will upload the provided, pre-processed PDB structures.

Expand Down Expand Up @@ -320,7 +320,7 @@ Then uncheck the option to automatically define passive residues as for the anti

### Job submission

This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *job_params* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload interface](https://bianca.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *job_params* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again. An excerpt of this file is shown here:
This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *job_params* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload interface](https://wenmr.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *job_params* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again. An excerpt of this file is shown here:

It can serve as input reference for the run. This file can also be edited to change a few parameters for example. An excerpt of this file is shown here:

Expand Down
16 changes: 8 additions & 8 deletions education/HADDOCK24/HADDOCK24-antibody-antigen/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ In this tutorial we will be working with Interleukin-1β (IL-1β) (PDB code [4I

<hr>

For this tutorial we will make use of the [HADDOCK2.4 webserver](https://bianca.science.uu.nl/haddock2.4){:target="_blank"}, [ProABC-2](https://wenmr.science.uu.nl/proabc2){:target="_blank"} and [PDB-tools webserver](https://wenmr.science.uu.nl/pdbtools){:target="_blank"}.
For this tutorial we will make use of the [HADDOCK2.4 webserver](https://wenmr.science.uu.nl/haddock2.4){:target="_blank"}, [ProABC-2](https://wenmr.science.uu.nl/proabc2){:target="_blank"} and [PDB-tools webserver](https://wenmr.science.uu.nl/pdbtools){:target="_blank"}.

A description of the previous major version of our web server [HADDOCK2.2](https://alcazar.science.uu.nl/services/HADDOCK2.2){:target="_blank"} can be found in the following publications:

Expand Down Expand Up @@ -69,7 +69,7 @@ Throughout the tutorial, coloured text will be used to refer to questions or ins

In order to run this tutorial you will need to have the following software installed: [PyMOL][link-pymol].

Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://bianca.science.uu.nl/auth/register/haddock](https://bianca.science.uu.nl/auth/register/haddock){:target="_blank"}.
Also, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. Use for this the following registration page: [https://wenmr.science.uu.nl/auth/register/haddock](https://wenmr.science.uu.nl/auth/register/haddock){:target="_blank"}.


<hr>
Expand Down Expand Up @@ -299,7 +299,7 @@ Save *output_1.pdb* as 4G6K_fv.pdb . If you wish to save the pipeline after this
### Registration / Login


If not provided with special workshop credentials, in order to start the submission you need first to register. For this go to [https://bianca.science.uu.nl/haddock2.4/](https://bianca.science.uu.nl/haddock2.4/){:target="_blank"} and click on **Register**.
If not provided with special workshop credentials, in order to start the submission you need first to register. For this go to [https://wenmr.science.uu.nl/haddock2.4/](https://wenmr.science.uu.nl/haddock2.4/){:target="_blank"} and click on **Register**.


To start the submission process, you are prompted for our login credentials. After successful validation of the credentials you can proceed to the structure upload under **Submit a new job**.
Expand All @@ -314,7 +314,7 @@ In previous steps we have identified the paratope residues of the antibody. Thos

#### Submission and validation of structures

For this we will make use of the [HADDOCK 2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
For this we will make use of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.

In this stage of the submission process we can upload the antibody structure we previously prepared with PDB-tools and the IL-1β structure.

Expand Down Expand Up @@ -398,7 +398,7 @@ Number of structures to analyze -> 400

#### Job submission

This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *haddockparameter* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload inteface](https://bianca.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *haddockparameter* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again.
This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *haddockparameter* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload inteface](https://wenmr.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *haddockparameter* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again.


* **Step 11:** Click on the **Submit** button at the bottom left of the interface.
Expand All @@ -414,7 +414,7 @@ In this scenario, additionally to the CDR residues of the antibody, a loose defi

#### Submission and validation of structures

We again make us of the [HADDOCK 2.4 interface](https://bianca.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.
We again make us of the [HADDOCK 2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1){:target="_blank"} of the HADDOCK web server.

In this stage of the submission process we can upload the structures we previously prepared with PyMOL.

Expand Down Expand Up @@ -479,7 +479,7 @@ Since we have a rather loose definition of the interface, we will input the corr

#### Job submission

This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *haddockparameter* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload inteface](https://bianca.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *haddockparameter* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again. An excerpt of this file is shown here:
This interface allows us to modify many parameters that control the behaviour of HADDOCK, but in our case, the default values are all appropriate. It also allows us to download the input structures of the docking run (in the form of a tgz archive) and a *haddockparameter* file which contains all the settings and input structures for our run (in json format). We strongly recommend downloading this file as it will allow you to repeat the run by uploading it into the [file upload inteface](https://wenmr.science.uu.nl/haddock2.4/submit_file){:target="_blank"} of the HADDOCK webserver. The *haddockparameter* file also serves as a run input reference. It can be edited to change a few parameters and repeat the run without going through the whole menu process again. An excerpt of this file is shown here:


* **Step 9:** Click on the **Submit** button at the bottom left of the interface.
Expand Down Expand Up @@ -695,7 +695,7 @@ These residues could be used as active residues for Interleukin-1β, leaving HAD
70,71,72,73,81,82,87,88,90,92,94,95,96,113,114,115
</pre>

The results of such a docking run can be found [here](https://bianca.science.uu.nl/haddock2.4/run/4242424242/4G6M-Ab-Ag-NMR-sas-filtered){:target="_blank"}.
The results of such a docking run can be found [here](https://wenmr.science.uu.nl/haddock2.4/run/4242424242/4G6M-Ab-Ag-NMR-sas-filtered){:target="_blank"}.

<a class="prompt prompt-info">
Inspect the results.
Expand Down
4 changes: 2 additions & 2 deletions education/HADDOCK24/HADDOCK24-binding-sites/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -250,12 +250,12 @@ For minocycline (called MIY in the PDB file):

#### Registration / Login

In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://bianca.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.
In order to start the submission, either click on "*here*" next to the submission section, or click [here](https://wenmr.science.uu.nl/auth/register/). To start the submission process, we are prompted for our login credentials. After successful validation of our credentials we can proceed to the structure upload.

#### Submission and validation of structures

Here we will launch a docking run using the apo form of the receptor (the renumbered PDB we just prepared) and rifampicin as potential ligand.
For this, we will make use of the [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1), using the *guru* level access (provided with course credentials if given to you, otherwise register to the server and request this access level [here](https://bianca.science.uu.nl/auth/register/).
For this, we will make use of the [HADDOCK2.4 interface](https://wenmr.science.uu.nl/haddock2.4/submit/1), using the *guru* level access (provided with course credentials if given to you, otherwise register to the server and request this access level [here](https://wenmr.science.uu.nl/auth/register/).

**Note:** The blue bars on the server can be folded/unfolded by clicking on the arrow on the left

Expand Down
Loading

0 comments on commit aadc32a

Please sign in to comment.