Alex's comments

Author: AnnaKravchenko

education/molmod_online/docking.md

@@ -204,7 +204,13 @@ solely on the evolutionary conservation analysis?
 
 ### Predicting interface residues
 
-Besides sequence conservation, another way to obtain information about possible interface residues is by analysing known interfaces found in **homologous** proteins.
+Besides sequence conservation, other features can be used to predict possible interfaces on protein structures. For example, certain residues tend to be overrepresented at protein-protein interfaces. This information, combined with evolutionary conservation and with a surface clustering algorithm that finds groups of surface residues meeting both the previous criteria results in reasonably accurate predictions. This is the basis of the [WHISCY](https://wenmr.science.uu.nl/whiscy/){:target="_blank"} server. A more advanced predictor, the [CPORT](https://alcazar.science.uu.nl/services/CPORT/){:target="_blank"} web server, judiciously combines (up to) 6 different predictors to provide a consensus prediction that is more robust and more reliable than any of the individual predictors alone. 
+
+Many tools in science are developed by dedicated PhD students and postdocs. Unfortunately, over time, some of these tools may become unavailable as maintaining and supporting them requires significant time and effort. In such cases, it may be necessary to use alternative tools.
+
+### Obtain known interfaces of homologous proteins
+
+Another way to obtain information about possible interface residues is by analysing known interfaces found in **homologous** proteins.
 This can easily be performed by [ARCTIC-3D](https://wenmr.science.uu.nl/arctic3d/){:target="_blank"}, a [tool](https://www.nature.com/articles/s42003-023-05718-w){:target="_blank"} dedicated to an automatic retrieval and clustering of interfaces in complexes from 3D structural information.
 As structural information of the human MDM2 interacting with other partners is available, ARCTIC-3D will extract interacting residues and cluster them into binding surfaces. Not all residues of a binding surface are relevant, as some amino acids may be rarely present among the interfaces that define that patch.
 Wisely define a probability threshold and note down the residue indices, as you will need them to define *active* residues in HADDOCK.

education/molmod_online/simulation.md

@@ -157,7 +157,7 @@ Take your time to know your system and what particularities its simulation entai
 
 <a class="prompt prompt-attention">
 You may have noticed that NMRBox is in the process of migrating its virtual machines from Ubuntu 20 to Ubuntu 24. The “Selecting an initial structure” section of this course was developed with Ubuntu 20 in mind and is currently not functional under Ubuntu 24. 
-However, Ubuntu 24 can be used for the rest of this part of the course.
+However, Ubuntu 24 can be used for the remaining of this part of the course.
 </a>
 
 In NMRBox, after you open the terminal prompt you notice `username@machine`, where your username is the same as the NMRbox username.
@@ -371,7 +371,7 @@ For capping to work correctly, **the input structure must include one additional
 (i.e. residues *−1* and *N+1* relative to the peptide of interest). 
 These residues act as placeholders and will be converted into caps. In practice, we add two glycine residues, 
 one at each end of the peptide sequence, before capping.
-Capping is performed with a python script `$MOLMOD_BIN/pdb_cap.py`, read it help message to learn how to use it:
+Capping is performed with a python script `$MOLMOD_BIN/pdb_cap.py`, read it's help message to learn how to use it:
 <a class="prompt prompt-cmd">
 python3.10 $MOLMOD_BIN/pdb_cap.py -h
 </a>
@@ -727,7 +727,7 @@ Despite dissipating most of the strain in the system, energy minimization does n
 temperature, and therefore velocities and kinetic energy. When first running molecular dynamics,
 the algorithm assigns velocities to the atoms, which again stresses the system and might cause the
 simulation to become unstable. To avoid possible instabilities, the preparation setup here
-describes several stages of molecular dynamics that progressively remove constraints on
+describes by includes several stages of molecular dynamics that progressively remove constraints on
 the system and as such, let it slowly adapt to the conditions in which the production simulation
 will run.