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
  • 9,846
6 votes

How to make 3d model of a protein that not exist in PDB?

No PDB Getting a crystal structure is hard work for crystallographers, even with a high throughput systems, so they make constructs with only known domains or regions of particular interest. What ...
Matteo Ferla's user avatar
  • 4,234
6 votes
Accepted

BinaryCIF vs MMTF formats, which one to choose?

So binaryCIF is newer and is heavily inspired by MMTF. NGL, the most "loved" JS library (IMO) to show protein fetches proteins as MMTF, while Mol* uses bCIF —Mol* has the official repo of ...
Matteo Ferla's user avatar
  • 4,234
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

JSmol - hide "JSmol" logo

OK, I got an answer here. Use: frank off to get:
Marcin Magnus's user avatar
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 : ...
pippo1980's user avatar
  • 1,043
4 votes
Accepted

Where can I visualize Ramachandran plot?

Here is a page with several suggested methods. I agree that Rampage looks the best of the options, but it seems that it provides some suggested workflows for drawing it in R so that it is very ...
Maximilian Press's user avatar
4 votes

How to draw a 3d structure using 3d coordinates from pdb file?

If you want to share a PDB file, you could try Michelanglo. It allows you to upload a PDB file (among other things) edit a description panel (which can feature special links that control the protein ...
Matteo Ferla's user avatar
  • 4,234
4 votes

How to draw a 3d structure using 3d coordinates from pdb file?

JSmol sounds like what you want - it'll let you display 3D structures from PDB files onto webpages using JavaScript. If you just want to view the structure rather than display them on webpages, there'...
Bioinfomrat's user avatar
4 votes

Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

I do not know if there is a function in Biopython.PDB for dihedral space transformations, but due to the lack of answers I would say no. Biopython.PDB is nice and clean, but I would use something with ...
Matteo Ferla's user avatar
  • 4,234
4 votes

Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

I answered about doing it with PyRosetta as I assumed that as BioPython PDB module is basic and the fact it was being asked made me think it was not possible. Turns out I was wrong. So I am making a ...
Matteo Ferla's user avatar
  • 4,234
4 votes
Accepted

Algorithm for counting neighbors

The usual method is dividing the space into cells, in your case 7Å cubes, assigning atoms to cells, and searching for neighbors only in 3x3x3=27 cells. This method is described in Wikipedia as cell ...
marcin's user avatar
  • 1,261
4 votes
Accepted

Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?

From google I got this as first hit : PDB_format_1992.pdf : Hopefully they keept the same Unit of measurement during the data/file format evolution/extension It seems the case for ...
pippo1980's user avatar
  • 1,043
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
  • 13.9k
3 votes
Accepted

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 ...
marcin's user avatar
  • 1,261
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 - ...
pazchem's user avatar
  • 41
3 votes
Accepted

Why am I not being able to detect all the bonds in a residue?

Your method doesn't work for two possible reasons; The radius information may be incorrect. Your molecule requires some minimization. This option helps to optimize distance between atoms. You can ...
SuleymanSelim's user avatar
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

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

There is some confusion in the question. Solvent accessibility of a residue, i.e. the area accessible to the solvent (water), depends on the 3D structure of the protein. It's not a property of an ...
marcin's user avatar
  • 1,261
2 votes

biological fluorescence supervised machine learing

Adding to Devon's correct answer: Depending on the amount of images you got, there is also the possibility to avoid the feature engineering by building a two level architecture: The first level ...
phngs's user avatar
  • 166
2 votes

biological fluorescence supervised machine learing

Whether to quantify things at all with depend on the technique you want to use. An end-to-end CNN (convolutional neural network) for example would just be fed the 3D image for training and predictions....
Devon Ryan's user avatar
  • 19.6k
2 votes
Accepted

How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

Dan is correct but it doesn't answer the question. After much thought, I have finally figured out how to do it, only thanks to Dan's answer. The problem is that a subsequence is one-dimensional and ...
Aalawlx's user avatar
  • 517
2 votes

How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

No, this doesn't makes sense (I think). The hydrophobicity of an AA is the hydrophobicity of the AA, in whatever context, just like it's molecular weight. It's weight is it's weight, in a structure ...
Dan's user avatar
  • 612
2 votes

Tool for predicting interactions in the cell

IBIS reports protein interaction with other biomolecules. Your protein or homolog must exist in the Protein Data Bank. IBIS @ NCBI: https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi "For a given ...
Aalawlx's user avatar
  • 517
2 votes
Accepted

Converter between PDB or mmCIF and MMTF

I wrote a very quick and dirty script to handle conversion between file types using BioJava. https://github.com/eedlund/Utils/tree/master/BioUtils Download the jar file here To run: ...
Rosalind Was Robbed's user avatar
2 votes

Converter between PDB or mmCIF and MMTF

You looked at this https://github.com/rcsb/mmtf-python "The python implementation of the MMTF API, decoder and encoder."
Marcin Magnus's user avatar
2 votes

Converter between PDB or mmCIF and MMTF

You can use PyMol to change the PDB to mmtf or other format. First open the PDB file and then choose file->export molecule-> choose which format you want to save as
NingNing Chen's user avatar
2 votes

Converter between PDB or mmCIF and MMTF

You can do this with BioStructures.jl in Julia. All the 6 transformations between PDB/mmCIF/MMTF are possible. For example, PDB to MMTF: ...
jgreener's user avatar
  • 931
2 votes

BinaryCIF vs MMTF formats, which one to choose?

Consider mmJSON. Each of the three PDB sites had the same problem: using mmCIF files in web-based viewers is inefficient. To solve this problem three new file formats were introduced: MMTF at RCSB, ...
marcin's user avatar
  • 1,261
2 votes

How to draw a 3d structure using 3d coordinates from pdb file?

I am not good as you are and needed to use a parser for the pdb file see https://mmcif.wwpdb.org/docs/software-resources.html: ...
pippo1980's user avatar
  • 1,043

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