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. ...
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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. ...
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  • 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
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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 ...
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  • 8,111
7 votes
Accepted

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 ...
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  • 1,066
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 ...
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  • 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 ...
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  • 315
6 votes
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What is the difference between Assignment and Prediction?

To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure ...
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  • 3,469
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 ...
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  • 385
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 ...
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5 votes
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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 ...
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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....
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  • 602
5 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 ...
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  • 3,469
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: ...
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  • 599
5 votes
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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 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 ...
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  • 11.7k
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 ...
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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 ...
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  • 429
4 votes
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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 ...
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  • 901
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

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 ...
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  • 901
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. ...
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  • 3,469
4 votes
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CCP4 file to a Python 3 numpy array or similar workaround

You can use Gemmi. ...
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  • 1,066
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 ...
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  • 901
4 votes
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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: ...
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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
3 votes

Do any publicly available databases detail protein structure and functional domains?

EnsEMBL also has this. Search for your gene of interest, choose your transcript, go to the page of its protein product(s), and select "Domains & Features" from the right-hand menu (using human p53 ...
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  • 8,111
3 votes
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Folded Protein Chunk Dimensional Classification?

CATH The CATH database classifies protein by fold: https://www.cathdb.info/ So the value from that is probably the most useful for you. Crystallographic conditions pH Salinity Dissolved Sugars ...
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  • 3,469
3 votes

Label protein strucuture residues in Chimera

You cant do this in Chimera, but in pymol you can write a script to do this. In terms of the view, you can use get_view on the command line. This returns a section that you can copy and paste in - ...
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  • 41
3 votes
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Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

Glycine has a single hydrogen atom as its side chain: All the six bond angles with the CA atom in the middle are about 109° (C-CA-N, C-CA-HA3, C-CA-HA2, N-CA-HA3, N-CA-HA2 and HA3-CA-HA2 using the ...
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