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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  • 7,957
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 ...
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  • 3,434
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 ...
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  • 3,434
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:
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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 ...
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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 ...
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  • 3,434
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'...
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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 ...
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  • 11.5k
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 ...
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  • 1,036
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
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 ...
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  • 3,434
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 ...
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  • 1,036
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 ...
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  • 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....
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  • 19.3k
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 ...
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  • 507
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 ...
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  • 602
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 ...
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  • 507
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: ...
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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."
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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
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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: ...
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  • 901
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, ...
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  • 1,036
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: ...
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  • 274
2 votes

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

As others said, there already exist javascript libraries to visualize a protein. The most complete and recent one would probably be Mol*, which is what is used on RCSB PDB website. Mol* actually works ...
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2 votes

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

Answer from @o-laprevote, converted from comment: Your protein includes intrinsically disordered regions (https://www.uniprot.org/uniprot/Q12802#family_and_domains). Showing a predicted structure may ...
2 votes

Generating 3D coordinates error

An ent file is a pdb file. Just change the extension. PDBe for example provides their PDB files as such.
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  • 3,434
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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  • 3,434
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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  • 3,434
1 vote

Best way to dock subset of protein PDB and definition of a ligand

Answer from @pippo1980, converted from comment: https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208 Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes

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