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Questions tagged [structural-biology]

For questions about modeling/predicting the structural of biomolecular entities (e.g. proteins, DNA/RNA, organelles, etc)

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Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...
PriZarah's user avatar
  • 409
2 votes
1 answer

How to calculate pharmacore features?

Cross-posted at Bioinformatics.SE. I want to use the enzyme ß-Glucuronidase with the pharmit database. I uploaded my file for the receptor from pdb file. How can I get the pharmacore features? So one ...
Andrea's user avatar
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5 votes
2 answers

An algorithm for implicit bond order and charge allocation for atomic coordinates?

I was wondering if there were any reliable algorithms out there that could allocate bond orders and formal charges of a given molecular structure if just the atomic coordinates (x,y,z) and atom type ...
Joshua Soon's user avatar
4 votes
1 answer

Force field for charged peptide-ion system

I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
Arete's user avatar
  • 195
2 votes
1 answer

How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?

I asked this at Biostars but the post seems to have been deleted there. My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
user366312's user avatar
  • 2,546
4 votes
2 answers

Non-Covalent Interaction between drug and DNA?

I am using classical molecular dynamics (MD) to observe a non-covalent interaction between my complex and the DNA, but there is a problem in that the complex interacts with the terminal of the DNA for ...
Abd-Elazeem Mohamed's user avatar
2 votes
1 answer

How to control the thickness of lipid bilayer with GROMACS

I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial. I can successfully orient the protein in the lipid (turquoise) as you can see in the image below: ...
littleworth's user avatar
  • 1,674
6 votes
2 answers

How to show orientation axis in Pymol

Is there a way to show the orientation axis in Pymol? It's something like this in VMD. I much prefer Pymol rendering.
littleworth's user avatar
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6 votes
2 answers

How are diffusion coefficients calculated?

To support my laboratory result, I'm searching for an MD/statistical mechanics approach to predict translational diffusion coefficients in the liquid phase. I'm aiming to describe small peptides and ...
Giuseppe Basile's user avatar
3 votes
1 answer

Domain decomposition error while applying bonded restraints - GROMACS

GROMACS version:version 2021.3-MODIFIED GROMACS modification: Yes Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up ...
Vasista's user avatar
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11 votes
2 answers

Where to find DNA structural atomic coordinates?

I need a code/app/website that can receive a DNA sequence, for instance AATCT, and output a file with the atomic coordinates. I used to do this on this website but the service is no longer working and ...
Carlos Andrés del Valle's user avatar
5 votes
0 answers

Simulating a circuit diagram for action potential [closed]

Cable theory is a good simulation for the resting potential. It imagines patches of cell membrane lipid bilayer as capacitors and transmembrane ion channels as resistors. But it seems this model is ...
user avatar
9 votes
1 answer

What is the purpose of DSSP when using martinize2?

I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...
Vranvs's user avatar
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9 votes
1 answer

What software can do RNA secondary structure prediction?

This question is a follow-up to this previous question. I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
rokamama's user avatar
  • 235
9 votes
1 answer

What software is a software for RNA tertiary structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
rokamama's user avatar
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25 votes
4 answers

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 ...
user37344's user avatar
  • 353
54 votes
3 answers

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, ...
ksousa's user avatar
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12 votes
1 answer

Why are condensed matter predictions considered on par with experiment, while structural biology modeling receives more skepticism?

I have two main modeling research lines: one related to structural biology (including rational drug design, de novo design, polymorphism, etc.) and the other one related to condensed matter (...
Camps's user avatar
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