All Questions
Tagged with proteins molecular-structure
15
questions
5
votes
0
answers
70
views
Do disulfide bonds determine the 3-dimensional structure of a protein or do they just stabilise the 3D structure?
I noticed that most disulfide bonds occur when two cysteine side chains exist in close proximity to each other. Do those cysteine side chains "look out" for each other during folding, that ...
- 107
1
vote
1
answer
681
views
Troubleshooting an AutoDock Vina error on Chimera: “Could not find an atomic number for Hn Hn”
After minimizing a ligand (prepared with MarvinSketch) and preparing a target enzyme to dock said ligand onto (collected from RCSP PDB — 5DGN (Crystal structure of human FPPS in complex with compound ...
- 467
0
votes
1
answer
83
views
What is "tail" in case of secondary structure of protein? [closed]
What is a "tail" in the case of the secondary structure of a protein?
How does it influence the "protein assignment" task?
user93950
3
votes
1
answer
601
views
How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?
When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
- 918
4
votes
3
answers
415
views
What is the difference between structure assignment and structure prediction?
I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning.
...
user93950
1
vote
0
answers
46
views
Is there a computer program capable of showing protein conformational changes based on pH?
As it is known, changes in pH change the attractions between the groups in the side chains of the protein.
Acidification can, for example, cause protonation of the $\ce{COO-}$ end to $\ce{COOH},$ ...
- 111
3
votes
1
answer
66
views
Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon
According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
- 1,264
0
votes
1
answer
799
views
How does X-Ray Crystallography determine the components (as opposed to the structure) of a molecule?
Thanks for some online resources (i.e. here) I have an understanding of what X-Ray Crystallography does.
By blasting X-Rays at a crystal and recording the scattering patterns on a plate behind the ...
- 311
3
votes
1
answer
1k
views
Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]
I am completely new to using OpenBabel software.
I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
7
votes
2
answers
3k
views
How to use Google’s Alpha-fold to predict the structure of a two-protein complex?
Alpha-fold won the CASP13 and CASP14 competitions last year and this year. It used deep learning to predict the secondary structure of a protein given the primary amino acid sequence.
Google has ...
- 924
1
vote
1
answer
269
views
What is the correct term of a chemical formula for very large molecules if not just "chemical formula"? [closed]
I know that many molecules, wihch I as a non chemist, might define as "small" if their two dimensional diagram can be sketched on an A4 page, are often formulated;
...
user61828
6
votes
3
answers
1k
views
What is the precise definition of Ramachandran angles?
The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
- 434
4
votes
1
answer
660
views
Why is casein hydrophobic?
According to this source hydrophobic behaviour occurs when a molecule does not have a charge or is neutral and therefore cannot be attracted to the negative nor positive parts of water. Casein has an ...
- 640
8
votes
1
answer
305
views
How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?
There are proteins with intrinsic symmetries. For example:
I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
- 924
2
votes
0
answers
140
views
RCSB PDB - how to choose between multiple copies of the same protein?
I want to map the location of missense mutations on a protein, SERPINB3. I intend to do this using PyMol and download the protein structure from RCSB PDB. However, ...
- 383