Questions tagged [3d-structure]
The 3d-structure tag has no usage guidance.
23
questions
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1answer
24 views
Site Mutations in a 3D protein structure to locate the core of mutations
I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations to see the hub of ...
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1answer
32 views
Intrinsically disordered protein
This question has also been asked on Biostars
The position that I have to visualize is in the 2700 position and this position exists in two ranges in https://www.uniprot.org/uniprot/Q12802#...
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0answers
42 views
3d model of a protein via nucleotide sequence
I really appreciate @Matteo Ferla's detailed answer to my previous question.
I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
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0answers
21 views
Best way to dock subset of protein PDB and definition of a ligand
I have extracted residue 45 to 88 from a PDB file (2YRQ).
With that I have a new smaller PDB file. Let's call it 45_88.pdb
And I want to dock it to some other full protein.
My question is what's the ...
3
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2answers
95 views
How to make 3d model of a protein that not exist in PDB?
I'm working on nsSNPs(Non-synonymous single nucleotide polymorphisms) of protein AKAP13 whose PDB not available.
I did one mutation in this protein and I want to show the effect by 3d modeling without ...
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1answer
23 views
Label and labelbox mismatched in Pymol after ray
I would like to ask how to overcome the problem of mismatched boxes and labels (pic). Is there an option focused on this?
thanks
Radim
2
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4answers
117 views
How to draw a 3d structure using 3d coordinates from pdb file?
I am trying to create a 3d structure from 3d coordinated from a pdb file.
I am trying to draw 3d coordinates from pdb file "ATOM 1 N VAL A 14 22.692 -27.591 -39.402" and using webgl ...
4
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1answer
57 views
BinaryCIF vs MMTF formats, which one to choose?
Both file formats are advertised as more memory/parsing efficent than old PDB format and its successor mmCIF format, but I can't understand the context (I'm a developer, but pretty new to the field of ...
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2answers
47 views
What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?
Since distant homologs often have significant structural changes, meaning the ...
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0answers
24 views
Extract only the amino acid residues on the surface of protein structure data
I'd like to use protein structure data from PDBs visualized by Chimera to do two things.
I'd be happy to learn the appropriate tools and methods.
・Mapping information about amino acids present on ...
0
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1answer
27 views
Generating 3D coordinates error
I have been trying to convert a multi entry sdf file to pdb using openbabel. Everytime I check the Generate 3D coordinates box I end up with .ENT files instead of .PDB files. What am I doing wrong.
...
2
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1answer
124 views
Where can I visualize Ramachandran plot?
I am using Rampage webserver to obtain a Ramachandran plot. However, the server does not reveal any plot just values (favored, allowed, outlier regions).
Can you recommend other similar web sites?
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1answer
77 views
What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?
I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
1
vote
1answer
125 views
Reconstruct a protein's 3D structure from a pair-wise distance matrix
What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues?
I think the question is self-explanatory. I know of this method
but it seems that it uses ...
1
vote
1answer
78 views
Which is the amino acids classification when analyzing the solvent accessibility of a protein?
I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
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vote
3answers
83 views
biological fluorescence supervised machine learing
Some general questions...
So it appears with most classification learners one must come up with a series of quantifiable variables to associate with each observation. This might include mean and std ...
3
votes
1answer
78 views
Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms
I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.
Specifically, I'd like to determine the ...
2
votes
1answer
136 views
Label protein strucuture residues in Chimera
I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Columbic electrostatic potential. I have opened them in two separate windows for comparison....
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2answers
98 views
How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?
I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY.
I ...
4
votes
1answer
64 views
JSmol - hide "JSmol" logo
I'm using JSmol for my SimRNAweb server. I would like to hide "JSmol" logo from all small visualizations that I have there. I would like to just put information about JSmol under the panel in text.
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0answers
69 views
Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]
This is an interesting problem - I was wondering if anyone has a creative solution.
So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
5
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2answers
121 views
Tool for predicting interactions in the cell
What tools are available to predict, based on the structure of a certain protein, its interactions within a cell?
For example, I am considering the split GFP protein and I am trying to predict if ...
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4answers
813 views
Converter between PDB or mmCIF and MMTF
I'd like to test MMTF, a new format for storing biomolecular structures which is promoted by RCSB as a more compact alternative to mmCIF and PDB.
From MMTF FAQ:
How do I convert a PDBx/mmCIF ...
