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Why are non-polar hydrogens neglected in protein-drug binding studies?

Why are (Non-polar) Hydrogen generally neglected in a protein-ligand (or drug) binding energy calculation? They do have charge and mass. Doesn't that affect the free energy calculation?
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2answers
37 views

Atomic coordinates for DNA bases as they appear in a B-form or A-form duplex

Where can I find atomic coordinates for guanosine / cytosine / thymine / adenine (either the ribonucleotide or deoxyribonucleotide bases) where the atoms are configured in the manner we would expect ...
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38 views

Modelling planar ring molecules and their evolutions

This is the next step of my previous question. I am trying to simulate a circular chain (ring) of molecules which are planar (two dimensional). What I do is take a planar unknot and embed it into a ...
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1answer
31 views

Modelling planar molecules and their evolutions

I am trying to simulate a chain of molecules which are planar. Can anyone please give me an example of the molecular chain which can stay as planar with it's minimum energy state is planar. A ...
0
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1answer
16 views

What conditions to use to crystallise Equine Myoglobin?

What are the crystallisation conditions for Equine Myoglobin? I've tried repeating some from the PDB but no success.
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2answers
94 views

Obtain chemical insight from neural network results

I have recently read many papers where neural networks (NNs) are trained to predict chemical properties (starting from the structure of small chemical compounds) for compounds rather close to the ones ...
5
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1answer
43 views

What is the appropriate method to visualize electrostatic potentials?

Using a molecular viewer like PyMOL, I understand that its often incorrect to simply look at positive and negative residues and use those residues to calculate the charge density and instead, you ...
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1answer
124 views

What chemical file formats are compatible with 3D printing?

I would like to print some molecules rather than building them using a kit. What file formats work?
5
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1answer
114 views

Why is it so difficult to create mock NMR spectra of macromolecules?

From what I understand, if you have a NMR spectra, you can determine the structure of a macromolecule but it is very difficult to determine what the NMR spectra of an expected structure would look ...
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248 views

What is Cβ (C-beta) deviation?

Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some ...
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1answer
602 views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)