Questions tagged [proteins]

For questions about modeling proteins

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What is the curve fitting model used for Qubit protein assay?

This is the example of Qubit protein assay curve. It relates the concentration (x-axis) with fluorescence (y-axis). What is the curve-fitting method it use for this? Clearly this is not simple linear ...
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2 votes
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What do we simulate with molecular simulation of proteins?

I know some: Secondary structure prediction Tertiary structure prediction protein-surface interaction test protein-protein interaction test protein-ligand binding test What else do we simulate? ...
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Open issues in MC protein simulation?

What are some open issues in Monte Carlo protein simulation research? I am especially interested in coarse-graining.
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2 votes
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20 views

How reliable is Alphafold2 for folding random-coil peptide

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
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5 votes
1 answer
79 views

Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides

This is a variation of a question asked on October 30, 2021 here, but it is different enough that I think it warrants a new post. I'm also trying to use RDKit. Is it possible to convert a SMILES ...
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5 votes
1 answer
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Why are ligands restrained when simulating a protein-ligand complex with MD?

Currently I'm doing an MD simulation of a protein-ligand complex using GROMACS. In the tutorial it mentioned the process of Restraining the Ligand. Why do we do it? Is it absolutely necessary?
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8 votes
1 answer
135 views

Alternative to CGenFF for generating large ligand topology

I am now preparing a ligand topology following GROMACS protein-ligand tutorial. However, I have a large ligand (446 atoms). $ wc -l my_ligand.pdb 446 my_ligand.pdb ...
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7 votes
0 answers
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How to determine minimum reasonable MD timing for ligand-protein complex [closed]

I am working on protein-ligand complex MD simulation using GROMACS. Now I'm running the tutorial. ...
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4 votes
0 answers
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A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
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9 votes
2 answers
861 views

How to calculate the computational time required for a MD simulation

I have a ligand and receptor to simulate with MD. These are my specs: Receptor has 4674 atoms, Ligand has 273 atoms CHARMM force field MD software GROMACS Computing machine: Amazon g4dn.xlarge (1 GPU ...
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6 votes
0 answers
85 views

How to show electrostatic interactions in Pymol or other 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 ...
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6 votes
0 answers
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How to look for specific structural motifs in proteins? [closed]

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 ...
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6 votes
3 answers
100 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.
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2 votes
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Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]

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"....
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6 votes
1 answer
62 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.
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6 votes
1 answer
227 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 ...
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6 votes
0 answers
37 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 ...
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4 votes
1 answer
73 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 ...
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10 votes
4 answers
172 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: ...
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5 votes
1 answer
67 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 ...
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6 votes
1 answer
45 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 ...
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8 votes
1 answer
166 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, ...
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  • 367
11 votes
1 answer
443 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 ...
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18 votes
1 answer
855 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 ...
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24 votes
4 answers
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 ...
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53 votes
3 answers
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, ...
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9 votes
1 answer
64 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 ...
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6 votes
1 answer
279 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 ...
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7 votes
1 answer
83 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 ...
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12 votes
1 answer
230 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 ...
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9 votes
1 answer
88 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 ...
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7 votes
1 answer
63 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 ...
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10 votes
2 answers
247 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 ...
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10 votes
1 answer
364 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 ...
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15 votes
1 answer
2k 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 ...
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15 votes
1 answer
101 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 ...
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