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10 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. ...
Iakov Davydov's user avatar
9 votes
Accepted

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. ...
Davidmh's user avatar
  • 206
9 votes
Accepted

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
Marcin Magnus's user avatar
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 ...
terdon's user avatar
  • 10.4k
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 ...
marcin's user avatar
  • 1,261
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 ...
Matteo Ferla's user avatar
  • 4,244
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 ...
Matteo Ferla's user avatar
  • 4,244
7 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 ...
CubeHead's user avatar
  • 425
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 ...
Aalawlx's user avatar
  • 527
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 ...
Nils's user avatar
  • 315
6 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 ...
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 ...
marcin's user avatar
  • 1,261
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 ...
Jannik M's user avatar
  • 106
5 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 ...
Abdul Ahad's user avatar
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 ...
Rosalind Was Robbed's user avatar
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 ...
Rosalind Was Robbed's user avatar
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....
Dan's user avatar
  • 612
5 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 ...
jgreener's user avatar
  • 941
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: ...
Mr_Z's user avatar
  • 629
5 votes
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Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

ok, here my input pdb, example_short.pdb : ...
pippo1980's user avatar
  • 1,195
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 ...
TW93's user avatar
  • 449
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 ...
gringer's user avatar
  • 14.7k
4 votes
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If I modify a PDB file with a specific mutation, how to minimize energy?

I would recommend you try the FoldX mutation engine. It is very easy to use and state of the art (it is the main competitor to expensive commercial software). It can do both of what you want - the ...
Aalawlx's user avatar
  • 527
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 ...
jgreener's user avatar
  • 941
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/.
Jonas Adler's user avatar
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

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
  • 4,244
4 votes
Accepted

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. ...
Matteo Ferla's user avatar
  • 4,244
4 votes
Accepted

CCP4 file to a Python 3 numpy array or similar workaround

You can use Gemmi. ...
marcin's user avatar
  • 1,261
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 ...
jgreener's user avatar
  • 941

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