Questions tagged [proteins]

For questions about modeling proteins

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2
votes
0answers
7 views

Construction of dimeric protein models, selection and refinement

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...
3
votes
1answer
22 views

Ligand-protein molecular docking with different protonation states

It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational ...
7
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0answers
23 views

Protein structure prediction

I want to perform a molecular docking between several ligands and the transmembrane domain of a protein. For this protein I only have the amino acid sequence, so it's necessary to do two things: ...
5
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1answer
25 views

How to interpret the affinity in a protein docking - ligand

I'm performing a molecular docking using a trans-membrane protein and several ligands. For the first ligand, the best conformation gave a binding energy of 110 kcal/mole, being 50 kcal/mole the ...
3
votes
0answers
14 views

Can we calculate the intermembrane protonation state?

I want to know the protonation state of the intermembrane subunit of a protein. For that, I need to know the pH, so given that small molecules can cross the lipid bilayer, could we assume intracelular ...
8
votes
1answer
96 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
11
votes
1answer
111 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...
17
votes
1answer
682 views

Does DeepMind's new protein folding software (AlphaFold) also work well for metalloproteins (proteins with metal cofactors)?

(1) Commonly, the metal is at the active site which needs the most prediction precision. (2) Typically, there is only one (or a few) metals in a protein, which contains far more other atoms. So, the ...
20
votes
3answers
1k views

Introduction to protein folding for mathematicians

My background is mostly in (applied) math with healthy doses of physics and computer science. Are there any good introductions to protein folding and its challenges for someone with that kind of ...
50
votes
3answers
8k views

DeepMind just announced a breakthrough in protein folding, what are the consequences?

There was some recent media reporting about a purported Google breakthrough on applying machine learning techniques to tackle the protein folding problem, as told for example in this news article, ...
9
votes
1answer
57 views

Finding conformations of peptide based on dihedral angles

I was trying to look at the alanine dipeptide trajectories from this link and track the trajectories in a Ramachandran plot. Below is a plot based on dihedral angles at each timestep for all ...
6
votes
1answer
121 views

Dihedral angles of alanine dipeptide

I have a number of trajectories of alanine dipeptide molecule and I'm interested in computing dihedral angles of each configuration. $\quad\quad\quad\quad$ Have I selected the right atoms for ...
7
votes
1answer
58 views

Protonation state of pdb ligand

I want to know the protonation state of some pdb ligands. For example, on the ligand, I want to know if the nitrogen is in its tertiary or quaternary form. I have been looking on the structure page ...
12
votes
1answer
107 views

How much of a difference in a protein's radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
9
votes
1answer
65 views

Docking proteins with glycans

Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
7
votes
1answer
52 views

Which non-commercial software can be used to dock two proteins?

I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below. Since there are many docking ...
10
votes
2answers
242 views

What are the factors to consider before docking 2 proteins?

With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
10
votes
1answer
134 views

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
14
votes
1answer
833 views

How to rectify the error “Lost atoms: original 28437 current 3659” in LAMMPS?

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
14
votes
1answer
87 views

How to characterize surface features in proteins?

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...