For questions related to the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function.

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4
votes
1answer
71 views

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 ...
4
votes
1answer
56 views

Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a ...
19
votes
2answers
655 views

Confusion about direction of dipole arrow in alpha-helices and other molecules

I understand that molecular dipoles are electric dipoles. And electric dipole moment vectors point from the negative to the positive charge. In class we learned to draw these special molecular dipole ...
1
vote
0answers
22 views

What are side chain order parameters?

I was reading an article: We first compared experimental (S 2 exp) and computed (S 2 calc) side-chain order parameters using the simplest approximation of side-chain conformational variability, ...
1
vote
1answer
33 views

Is it possible to identify the source of a protein hydrolysate [closed]

I have a powder which only declares to be "Protein Hydrolysate" Meaning that the all the protein has been broken down. We've tried to identify the source of the powder with DNA research. But no ...
0
votes
0answers
62 views

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

Why are (non-polar) hydrogen atoms 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? The ...
2
votes
2answers
142 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 ...
1
vote
0answers
45 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 ...
0
votes
1answer
45 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
votes
1answer
26 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.
4
votes
2answers
107 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
votes
1answer
49 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 ...
13
votes
5answers
583 views

Are there notable organic compunds which look very similar but have very different properties?

I've seen people arguing for some questionable "miracle cure-all" alternative medicines not scientifically, but by their own logic. A common claim is, that if a compound looks very similar to an ...
7
votes
1answer
181 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?
6
votes
1answer
138 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 ...
15
votes
1answer
548 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 ...
21
votes
1answer
1k 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)
15
votes
2answers
766 views

How large is the energy difference between keto- and enol-form of guanine and uracil?

The nucleobases in DNA and RNA are generally present in the keto-form, and not in the enol-form. As an interesting historical note, James Watson and Francis Crick did initially believe them to adopt ...