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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13
votes
1answer
70 views
+50

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
18 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, ...
0
votes
0answers
36 views

How many molecules would there be in the complex? [closed]

The question is: If a protein formed a complex with octahedral symmetry, how many molecules would there be in the complex?
0
votes
1answer
30 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
52 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
55 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
44 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
40 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
25 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
104 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
48 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 ...
7
votes
1answer
160 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
128 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 ...
14
votes
1answer
417 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 ...
20
votes
1answer
928 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)