6 votes
Accepted

BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure

The problem got solved after posting on the official BioPython repo. Because of the processing (where some residues were removed in order to align the proteins), some consecutive residues were too far ...
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  • 385
5 votes
Accepted

What tool RCSB and AlphaFold use to visualize 3D structures?

Different criteria give different rankings. Mol* (read molstar with trilled rhotic R according to the given IPA) is the newest, is used by the RCSB PDB and can ...
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, ...
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  • 71
4 votes

Database for proteome-wide predictions of protein structures

By far the most accurate model right now should be AlphaFold, and there are open structures across several proteomes available at https://alphafold.ebi.ac.uk/.
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4 votes
Accepted

What is the function of the heteroatoms

The text you cited mentions "input structure", so they work with structures, not just "protein sequences". Heteroatoms = atoms marked as HETATM ...
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  • 1,091
3 votes

What is DSSP algorithm for?

"Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone" (source) To be more specific: ...
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3 votes
Accepted

How to represent a summary of disagreement between two secondary structure predictors given predictions for many proteins?

(This comment got too long) positions in a predicted protein chain You do mean position in SS sequence, not coordinates in tertiary, yes? From the sounds of it you are talking about SS —not tertiary—...
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  • 3,719
3 votes
Accepted

Identify side chain atoms in BioPandas dataframe

As you suggest one way of solving your problem would be by selecting all atoms that don't have backbone atoms names. In a pdb file I believe backbone atoms would be named 'CA', 'HA', 'N', 'HN' or 'H', ...
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3 votes
Accepted

What does it mean by "PC" in this article?

Answer from @user438383, @matteo-ferla and @m, converted from comments [anyone, feel free to edit this answer to improve it]: According to the intro it means 'pseudocenter'. All measurements are ...
2 votes
Accepted

Different structures of same protein from two softwares

Superposition https://michelanglo.sgc.ox.ac.uk/data/d6e427bb-a0cb-4a65-b988-b08237f5054a SwissModel https://swissmodel.expasy.org/repository/uniprot/Q969F8 SwissModel models are threaded against a ...
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  • 3,719
2 votes
Accepted

Does the Protein Data Bank contain the estimated distances obtained using NMR spectroscopy?

The data can be found here: https://bmrb.io/search/instant.php?term=2KB7 There is no link directly in the PBD as it is a one-to-many relationship. Clicking on the first value (a shifts dataset) you ...
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  • 3,719
2 votes
Accepted

GROMACS RMSF Result Analysis Problem

The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the ...
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  • 507
2 votes
Accepted

What does the following diagram represent?

Yes, the letters are amino acids It's a schematic with a whole residue as a circle —possibly from Voet and Voet. Residue i is the one in focus, the reference. ...
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  • 3,719
2 votes

PyMol: Output Polar Contacts Between Chains to Text File

So you can install PyMOL as a standalone, but you can also install it as a bona fide Python 3 module via conda: ...
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  • 3,719
2 votes

Permutations of 4 amino acid sequence oligopeptide

The Python solution is here. IMO Bash definitely isn't a good solution for this calculation. ...
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  • 7,721
2 votes

How to extract part of protein complex separated with HEADER with two molecules from one PDB file

Since this is not a correct PDB file, it can be interpreted differently by different PDB reading libraries. The most reliable way to change it would be to read it as plain text and change the chain ID ...
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  • 1,091
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 ...
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  • 3,719
2 votes

Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

not able to grasp the question, tried to figure out a way to show the internal_coordinates: ...
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  • 330
2 votes
Accepted

How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

There are three options: it's a badly phrased Ramachandran plot question it's a question aimed at the describing the properties of different SS it's a trick question φ & ψ can be used to ...
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  • 3,719
2 votes

How do I build a glycosylated protein from PDB files manually?

You can use ChimeraX. Open your glycans and your protein pdb files as different models, then move the models of your glycans until they are near the residues you want (in the Toolbar: Right Mouse -&...
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2 votes

What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?

This is a common Q. Briefly, you have some techniques here that get used separately or combined: Ab initio: assemble the protein from scratch, often via a library fragmented peptides (3-mer, 6-mers, ...
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  • 3,719
2 votes

How reliable is Alphafold2 for folding random-coil peptide

Possibility 1: technical error AlphaFold2 uses MSA to infer residue co-evolution (due to epistasis) and thus proximity. A MSA can become contaminated with incorrect homologues, especially shorter ...
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  • 3,719
2 votes
Accepted

Protein-Ligand in PDB

In some protein crystallography studies, the protein crystals are grown with the substrate/ligand/inhibitor added, thus the resulting structure contains both the ligand and the protein atom ...
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  • 136
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
Accepted

Perform protein structure-based sequence alignment in Python

PyMOL in itself can be used as python package. The GUI app has its own Python, but in a conda environment you can install it as a package. Any PyMOL app command can be used as a cmd command. In PyMOL ...
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  • 3,719
1 vote
Accepted

Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

It turns out that in order to generate the internal coordinates for a protein structure, one shouldn't manually create an IC_Chain object, but rather just use the <...
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  • 385
1 vote

How do I build a glycosylated protein from PDB files manually?

answer from @coot, converted from comments (please edit this answer to improve it if you can): Manual model building is a common thing in structural biology. Usually, Coot is used.
1 vote

Help me in understanding the PDB file

well wasnt able to figure out how to make openapigenerator work with rcsb pdb ModelServer https://models.rcsb.org/, I ended up with this code copying the webserver manual input results for ligands: <...
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  • 330
1 vote

Permutations of 4 amino acid sequence oligopeptide

Here's a bash solution using brace expansion and the single-letter codes for the 20 common amino acids: ...
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  • 463
1 vote

How to make MSA for contact prediction?

You might have some luck with Parsnp. From the description: Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be ...
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