All Questions
Tagged with proteins computational-chemistry
9
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When optimizing AMBER molecular dynamics parameters for protein-ligand interactions, how do I balance accuracy and efficiency?
Are there established practices for fine-tuning AMBER MD parameters in scenarios like mine, involving specific factors like mutant proteins or non-standard ligands? Has anyone successfully tackled ...
1
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1
answer
681
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Troubleshooting an AutoDock Vina error on Chimera: “Could not find an atomic number for Hn Hn”
After minimizing a ligand (prepared with MarvinSketch) and preparing a target enzyme to dock said ligand onto (collected from RCSP PDB — 5DGN (Crystal structure of human FPPS in complex with compound ...
- 467
1
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2
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105
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To which extent is protein folding conserving subprotein structures?
I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
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2
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308
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How would I make a basic protein folding algorithm? [closed]
On the face of it it doesn't seem especially difficult.
Model the amino acids as solid objects linked together. Approximate the 3D force fields around them using a coarse approximation, then set the ...
- 175
5
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2
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913
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Generating electron density from protein coordinate (PDB)
Normally protein coordinates are generated from electron density, such as that from X-ray scattering experiment. In my case, I want the reverse - PDB to electron density mesh. I thought it was more ...
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Calculating the energy of a molecule using probability distributions
I wish to calculate the energy for a protein where the position of all the C-alpha atoms is known.
One way is to calculate the pairwise distances between the atoms and then look up a probability ...
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6
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1
answer
1k
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How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
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1
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1
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439
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How can absolute binding free energies be calculated?
In the calculation of binding free energies, such as between a protein and a ligand, I learned that absolute values cannot be obtained from simulation (such as taught in this lecture, slide 2). Rather,...
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4
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How to connect proteins via disulfide bonds computationally?
I want to connect proteins together to form a dimer. As seen in the picture, the monomers come close to each other along the edge of the higher-order structure (forget about the sulfate there). How ...
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