Questions tagged [structural-biology]
Questions relating to the structure (3-D conformation) of biological molecules, such as protein, RNA and DNA.
23
questions
0
votes
2
answers
73
views
Pymol: select low confidence regions from AlphaFold pdb file
I have downloaded a predicted structure from AlphaFold as a pdb file (https://alphafold.com/entry/O75376) and loaded it into Pymol (2.3.0). There is quite a large portion of the structure that was ...
- 259
3
votes
1
answer
42
views
How to visualize electron density of a specific part of the protein residue?
Hi everyone (mostly who are interested in structural bioinformatics).
I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a ...
1
vote
0
answers
21
views
How to identify different protein domains using HHpred
I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using ...
1
vote
1
answer
123
views
How to show electrostatic interactions in Pymol on the wanted residue
I have the following Pymol visual,
The green molecule is receptor and red/yellow is the ligand.
In the ligand I highlighted Lysine (K) residue as yellow.
What I want to do is to highlight and draw ...
- 155
1
vote
1
answer
171
views
Python script to simultaneously generate multiple pdbqt files for AutoDockTools?
I have a folder of pdb ligand structures that I'd like to test in some docking experiments with a certain protein using AutoDock Vina.
I am not familiar with Python so I've always been using the ...
- 11
0
votes
1
answer
35
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#...
- 81
1
vote
1
answer
40
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 ...
- 131
3
votes
1
answer
281
views
Programmatically adding hydrogen and remove water to multiple PDB files
I'm trying to dock a ligand to several hundred PDB files (receptors).
I thus need to prepare the those PDB files like removing water and adding hydrogen.
I can do that manually using Autodock or Pymol....
- 155
2
votes
1
answer
144
views
How to tell if our ligand-protein docking is good from AutoDock Vina's result
I have perform a ligand-protein docking using Autodock Vina.
The result of the docking looks like this:
...
- 155
0
votes
1
answer
37
views
Holistic enzyme activity determination with computation [closed]
I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
0
votes
2
answers
50
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 ...
- 21
1
vote
1
answer
502
views
Combine structures in the same session - PyMOL
I'm a student currently looking at antibody responses against a viral target protein of interest.
I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
- 11
1
vote
1
answer
99
views
Outputting crunchable list of HBonds from Pymol
X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?)
I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am ...
- 21
1
vote
1
answer
189
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 ...
- 25
4
votes
1
answer
208
views
How did researchers derive the Ramachandran "validation" contours?
I'm a beginner to structural biology and for fun, calculated the tortional angles of some 100, 000 proteins. Here is my Ramachandran plot:
When I went to look for "canonical" Ramachandran plots, I ...
- 141
0
votes
2
answers
104
views
What is the difference between fixed effects and random effects in the context of Linear-mixed models?
The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
- 186
1
vote
1
answer
764
views
Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?
Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations.
Specifically helping screen existing drugs against ...
- 11
2
votes
2
answers
1k
views
Is there a Python package to convert InChi to molecular structures?
I am looking for a python package that can convert InChi keys (e.g.SGNXVBOIDPPRJJ-UHFFFAOYSA-N) to molecular structure or SMILES strings. Can I do that with RDKit?
The key comes from: https://www....
- 1,181
3
votes
2
answers
597
views
Putting labels of different sizes on one PyMOl Object
I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
- 41
0
votes
2
answers
124
views
What is the best way to start with Structural bioinformatics with zero prior experience? [closed]
My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to ...
- 145
5
votes
3
answers
1k
views
Why is it necessary to add hydrogen and delete water before protein-ligand docking?
What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
- 189
5
votes
0
answers
63
views
What is a sensible forcefield choice for membrane proteins when using PDB2PQR?
I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. The goal is to calculate the electrostatic charge across the surface of the protein. There are no ...
- 399
3
votes
1
answer
67
views
predict the foldability of single-stranded DNA molecules
I have a list of regions of the human genome and I want to predict if single-stranded molecules in a buffer would tend to fold and create pin structures by sequence self-complementarity. What's the ...
- 2,234