4
votes
Why is it necessary to add hydrogen and delete water before protein-ligand docking?
Hydrogens
Most crystallographic structures are X-ray and the hydrogens are absent. In the case of neutron diffraction models, there may be many missing high b-factor ones (example in PDB:5MOP). As a ...
- 4,274
4
votes
Why is it necessary to add hydrogen and delete water before protein-ligand docking?
My answer is mainly based on molecular dynamics,but in this context it shouldn't make much of a difference.
The main reason has to do with the force-field-...
- 577
4
votes
File I/O error using nglview.show_biopython(structure)
I also figured out another way to fix this problem. After going back to the tutorial I was talking about I saw that it was made back in 2021. After seeing this I wonder if we were using the same ...
4
votes
How to show electrostatic interactions in Pymol on the wanted residue
Depends whether you work with named selections which is preferable and helpful if you want to use this Pymol session for future images. In this case, use the distance command for your two selections, ...
- 71
4
votes
What is the correct method of identifying the interacting residues for specific molecular docking?
Not an answer either. But a series of caveats.
First, HEM parameterisation. For molecular thermodynamics tools you will need to generate a topology file for this ...
- 4,274
3
votes
What is the correct method of identifying the interacting residues for specific molecular docking?
not an answer, just more inputs, but https://proteins.plus/5tl8#poseview
gives me this:
references:
ProteinsPlus: interactive analysis of protein–ligand binding interfaces
Molecular complexes at a ...
- 1,299
3
votes
File I/O error using nglview.show_biopython(structure)
This is an issue with Biopython 1.80, in particular introduced by a commit that automatically closes IO objects sent to PDBIO.save.
I made a PR to change the ...
- 951
3
votes
3
votes
How did researchers derive the Ramachandran "validation" contours?
To expand on Matteo Ferla's comment as an answer, there are two approaches to getting these "allowed" contours:
From probabilities found in observed crystal structures. You could imagine plotting a ...
- 951
3
votes
Accepted
Intrinsically disordered protein
Asking how to visualise the disordered region of a protein is a bit like asking how to visualise the location of an electron.
An intrinsically disordered protein, by definition, has regions that are ...
- 15.1k
3
votes
Accepted
Is there a Python package to convert InChi to molecular structures?
Yes, RDKit can be used, however, if you installed it with conda it will not work out of the box for inChi key fetching. You can either spend some time installing ...
- 4,274
3
votes
Accepted
What is the correct method of identifying the interacting residues for specific molecular docking?
I think I've found the answer to my own question.
So, I tried using this PRANK web server for predicting the binding site of my protein. The results is suprisingly very similar to the one from the ...
- 61
2
votes
Putting labels of different sizes on one PyMOl Object
'label_size' is a object-state-level setting, which means that you will have to rely on the 'create' command to create a new object for every different label size.
It can certainly be automated, and ...
- 71
2
votes
What is the best way to start with Structural bioinformatics with zero prior experience?
As others have said, there is no short cut and you will need to spend some time with a good book.
I would say there are 3 broad areas of understanding you have to have as a structural ...
- 951
2
votes
Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?
There are a few steps in between pdb and .maps.fld.
Here is the list of several scripts that can do tasks for you that you ...
- 4,274
2
votes
Is there a Python package to convert InChi to molecular structures?
Slightly modified Matteos answer:
...
- 1,305
2
votes
Programmatically adding hydrogen and remove water to multiple PDB files
I believe PDB2PQR CLI will do the work wonderfully. Don't let the name trick you: PQR files are organized like PDB ones. Under the hood it runs propka, which is state-of-the-art for predicting a ...
- 493
2
votes
How to tell if our ligand-protein docking is good from AutoDock Vina's result
It is best to contextualise the numbers. -1 kcal/mol is about the potential energy gained from a hydrogen bond —technically described in the r^6 part of the Lenard–Jones term, it is also the average ...
- 4,274
2
votes
Accepted
Pymol: select low confidence regions from AlphaFold pdb file
Answer from @matteo-ferla, converted from comment:
They are stored as b-factors. This is well described in the PyMol wiki.
[please edit to improve this answer, if possible]
2
votes
How to visualize electron density of a specific part of the protein residue?
NGLview runs off the JavaScript libray NGL, which is documented as a series of very helpful examples: in the gallery. The commands are not one-to-one (slightly frustratingly), but it is helpful as you ...
- 4,274
2
votes
Accepted
What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?
The difference between different force-fields is not going to be major, it is the side steps which are.
When
If you are starting from a SMILES string, optimisation is a must obviously.
If you are ...
- 4,274
2
votes
Accepted
How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?
You can check specification of pdbx_seq_one_letter_code and pdbx_seq_one_letter_code_can. These items are generated from the depositor-provided sequence on the PDB side. I suppose that the software ...
- 1,306
2
votes
How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?
So, i was little myopic when reading the PDB description the first few times, but roughly what i was looking for is this:
the non-canonical sequence(...
- 374
1
vote
File I/O error using nglview.show_biopython(structure)
tried to understand git, I ended up with this, seems more coherent with the previous habits in the biopython project, but cant push it.
Anyone could pass it along ? [of course needs to be checked out,...
- 1,299
1
vote
Python script to simultaneously generate multiple pdbqt files for AutoDockTools?
Answer from @matteo-ferla, converted from comment:
If command line interface is more suitable for you, you may consider OpenBabel, which can predict Gasteiger charges, protonate at pH 7, accept a smi ...
1
vote
Best way to dock subset of protein PDB and definition of a ligand
Answer from @pippo1980, converted from comment:
https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208 Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes
1
vote
What is the difference between fixed effects and random effects in the context of Linear-mixed models?
I do not know much about statistics but I will try my best to explain.
First, random effects are defined as the factors (categories) in the population that we are not aware of (not observed), so we ...
- 887
1
vote
Holistic enzyme activity determination with computation
Your title says holistic. This is a tad problematic as there's layers upon layers. Say, post-translation regulation, inhibiting metabolites, interacting protein etc....
- 4,274
1
vote
What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
TM-align has some options to do this, see for example https://zhanglab.ccmb.med.umich.edu/TM-align/help.html.
TM-align is similar to TM-score but the alignment is purely structural.
- 951
1
vote
Combine structures in the same session - PyMOL
Open the PyMOL session.
Use the load command to load your PDB file(s): load file.pdb.
Use the ...
- 951
Only top scored, non community-wiki answers of a minimum length are eligible