Questions tagged [proteins]

For questions about modeling proteins

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4
votes
0answers
18 views

How to look for specific structural motifs in proteins?

Is there a way to search to search for specific structural motifs in proteins? For example can a database where we can find structures with zing finger motif or an hairpin... PDBeMotif (ebi.ac.uk) has ...
5
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3answers
78 views

How to extract specific frames/model from a multi model pdb file?

I have a multi model pdb file and would like to extract the last frame or any other frame from it.
2
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0answers
38 views

Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme?

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
6
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1answer
55 views

How are tertiary protein structures represented in computers?

What data structure is used in representing protein structures in computers so that we can apply algorithms? Matrix or Graph or tree? P.S. I am absolutely new to Bioinformatics.
6
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1answer
81 views

Secondary structure information at each frame in a VMD trajectory

I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list to calculate the secondary structure ...
6
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0answers
36 views

Construction of dimeric protein models, selection and refinement [closed]

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 ...
4
votes
1answer
38 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 ...
10
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4answers
145 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
31 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 ...
6
votes
1answer
44 views

Can we assume that the intraceullular pH and intermembrane pH are the same when calculating the protonation state of a protein subunit?

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 ...
8
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1answer
125 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
245 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 ...
18
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1answer
772 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
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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 ...
51
votes
3answers
9k 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
62 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
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1answer
185 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
63 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
134 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
73 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
59 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
246 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
237 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
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1answer
1k 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 ...
15
votes
1answer
91 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 ...