All Questions
Tagged with proteins structural-biology
11
questions
2
votes
2
answers
139
views
How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?
So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
- 381
2
votes
1
answer
499
views
Is a beta pleated parallel sheet always formed from more than one peptide?
I can conceptually grasp the beta pleated anti-parallel sheet by imagining a curved length of string i.e. one polypeptide, starting with the N- terminus on the left and ending with the C-terminus at ...
- 267
3
votes
1
answer
1k
views
Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]
I am completely new to using OpenBabel software.
I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
8
votes
1
answer
305
views
How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?
There are proteins with intrinsic symmetries. For example:
I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
- 924
6
votes
1
answer
206
views
Biomolecular energy functions and entropy
From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
- 163
4
votes
2
answers
583
views
How to measure distance along solvent-accessible surface of protein complex in PDB file?
I am looking for a straightforward way to measure the distance between two active sites in a protein complex (PDB file).
I need the distance along the solvent-accessible surface of the protein and not ...
- 313
17
votes
2
answers
4k
views
What makes heat resistant proteins heat resistant?
We were doing the chapter Biomolecules in class the other day, and a doubt popped up once we reached the section on proteins.
We were taught that the stuff that keeps proteins together are: Ionic ...
- 18.8k
9
votes
4
answers
3k
views
Does quantum mechanics play a role in protein folding?
Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. However, for the initial micro-steps of folding, when an atom, or a configuration of atoms, can ...
- 101
5
votes
1
answer
418
views
Is the structure of a crystalized protein the native one?
When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
user28429
4
votes
1
answer
137
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 ...
- 662
5
votes
1
answer
235
views
Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)
I just learned that charged alpha helices are less thermally stable than uncharged ones. The only difference I see between them would be a larger dipole moment in the charged helix, but how would this ...
- 662