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 ...
Matteo Ferla's user avatar
  • 4,234
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-...
fra's user avatar
  • 567
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 ...
Jeremiah Wade's user avatar
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, ...
bunher's user avatar
  • 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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
pippo1980's user avatar
  • 1,088
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 ...
jgreener's user avatar
  • 941
3 votes

File I/O error using nglview.show_biopython(structure)

I had a similar problem with: ...
pippo1980's user avatar
  • 1,088
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 ...
jgreener's user avatar
  • 941
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 ...
gringer's user avatar
  • 14.1k
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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
Dembappe's user avatar
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 ...
bunher's user avatar
  • 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 ...
jgreener's user avatar
  • 941
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 ...
Matteo Ferla's user avatar
  • 4,234
2 votes

Is there a Python package to convert InChi to molecular structures?

Slightly modified Matteos answer: ...
Soerendip's user avatar
  • 1,295
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 ...
O.Laprevote's user avatar
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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
marcin's user avatar
  • 1,261
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(...
rtviii's user avatar
  • 364
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,...
pippo1980's user avatar
  • 1,088
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 ...
Phoenix Mu's user avatar
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....
Matteo Ferla's user avatar
  • 4,234
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.
jgreener's user avatar
  • 941
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 ...
jgreener's user avatar
  • 941

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