9
votes
How can we find the distance between all residues in a PDB file?
If you need to process multiple files, you could use Biopython to parse a PDB structure.
...
- 2,715
9
votes
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How to select high quality structures from the Protein Data Bank?
There is a very nice database, pdbcull (also known as the PISCES server in the literature). It filters the PDB for high resolution and reduced sequence identity. It also seems to be updated regularly. ...
- 206
9
votes
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Getting structure and sequence related to PDB IDs
You can download seqs and structures based on a list of PDB ids using http://www.rcsb.org/pdb/download/download.do#FASTA
- 676
7
votes
Tool for predicting interactions in the cell
You could try one of these tools to predict protein-protein interactions:
Struct2Net
Given two protein sequences, the structure-based interaction prediction technique threads these two sequences to ...
- 9,352
7
votes
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What does the yellow mean in this image from Virus Pathogen Resource?
Sulfur atoms are shown in yellow.
The molecular viewer that you use is JSMol (JMol ported to the web).
Atoms are colored by element: grey C, blue N, red O and yellow S.
If you wonder how other atoms ...
- 1,176
7
votes
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Generate ligands candidates based on protein shape
TL;DR: docking is much slower than any ML approach, but the ML approach can be constrained by pharmacophores dictated by the active site.
Side note: Scale
The scale for ligand space exploration is ...
- 4,124
7
votes
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What is protein secondary structure assignment?
To make it crystal clear (and make than pun):
Assignment: a 3D structure is known and the residues are assigned a secondary structure
...
- 4,124
6
votes
Best distance parameter for estimating physical interaction between residues in a PDB file
A popular (and I would say, respected and trusted) website is PDBsum https://www.ebi.ac.uk/pdbsum (which also has a Wikipedia article about it: https://en.wikipedia.org/wiki/PDBsum)
They measure ...
- 507
6
votes
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Do any publicly available databases detail protein structure and functional domains?
Some of this information (at least some domains, active sites, etc) is available from UniProt.
If you want to download their whole database, you can search without specifying any terms and then click ...
- 315
6
votes
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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 ...
- 405
6
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 ...
- 1,176
6
votes
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Why do we need to find minimum energy in a protein chain?
After translation, proteins fold to achieve a specific 3D structure which allows them to perform their specific functions. The structure of a protein computationally inferred through energy ...
- 76
5
votes
How to select high quality structures from the Protein Data Bank?
If you choose to perform your own culling of the PDB, resolution is probably the first thing you'll want to look at, which as Davidmh mentions is the main selection criteria for PISCES. High quality ...
5
votes
Accepted
Phyre2 vs ITasser, completely different models generated
I'm less familiar with Phyre, but I-TASSER is a really sophisticated system that takes the results of a search using multiple threaders and plugs them into an ab initio simulation which tries to ...
5
votes
how to find the bound form of an enzyme structure?
Tried looking for an explicit database? i.e.
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder: https://www.ncbi.nlm.nih....
- 602
5
votes
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Get protein names corresponding to PDB ID
You can use one of the UniProt Protein APIs.
As you said you have your pdb entries in a text file line by line you can, like this example.txt containing:
...
- 629
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 ...
5
votes
Accepted
Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file
ok, here my input pdb, example_short.pdb :
...
- 783
4
votes
how to find the bound form of an enzyme structure?
Are you aware of BRENDA? I was just introduced to it today for a completely separate reason (looking at carbohydrate enzyme families in the Nippostrongylus brasiliensis proteome), and it seems to be a ...
- 13k
4
votes
If I modify a PDB file with a specific mutation, how to minimize energy?
Yes you can modify the reference PDB file and look for the changes and for this purpose you need visualizers. One among these is Chimera. You can easily carry out the energy minimization steps using ...
- 41
4
votes
How can we find the distance between all residues in a PDB file?
Could you use CCP4's NCONT program? There's a GUI and a command line interface, whatever suits. You can specify which chains you want to target and interact with and set a cut off for distance. The ...
- 439
4
votes
Accepted
Database for proteome-wide predictions of protein structures
There are three initiatives I know of to have a go at this:
PConsFam, which collects data from this paper.
The Baker group's metagenomic study which you mention in the question.
The recent DMPfold ...
- 931
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/.
- 141
4
votes
How to quickly and robustly convert between mmCIF and PDB?
Converting a PDB file to some version of an mmCIF file is always possible provided the PDB file doesn't have any "problems". However grouping identical molecules into the same entity is non-trivial so ...
- 931
4
votes
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Extract autodocked protein-ligand connections programatically
With pymol as a python module (conda install -c schrodinger pymol, not the GUI one), it is very easy.
...
- 4,124
4
votes
Accepted
4
votes
How does sequence alignment help with protein folding prediction?
Protein sequences from the same family form a sequence alignment. Some positions in the alignment will be conserved, i.e. the same in all sequences. These are often associated with function, e.g. a ...
- 931
4
votes
Accepted
How to extract subset of protein structure (PDB format) file based on a subsequence of that protein
In general, if you simply want to extract that part of the PDB file, you could loop over it (it's plain text) and check the fields you're interested in:
...
- 156
4
votes
Accepted
How are tertiary protein structures represented in computers?
comments from above fleshed out.
Both: A graph network is a handy way to represent a molecule, but a matrix makes for fast maths.
A graph network is a list of nodes...
- 4,124
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
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