Questions tagged [protein-folding]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2 votes
1 answer

How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?

I asked this at Biostars but the post seems to have been deleted there. My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
4 votes
0 answers

How reliable is Alphafold 2 for folding random-coil peptide [closed]

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
2 votes
0 answers

How can I calculate the radius of a residue? [closed]

I want to read a PDB file and display/render the atoms using a graphics engine. If I consider each residue in the protein file as a solid sphere, what would be the radius of the sphere? How can I ...
25 votes
4 answers

Introduction to protein folding for mathematicians

My background is mostly in (applied) math with healthy doses of physics and computer science. Are there any good introductions to protein folding and its challenges for someone with that kind of ...
10 votes
4 answers

Protein structure prediction

I want to perform a molecular docking between several ligands and the transmembrane domain of a protein. For this protein I only have the amino acid sequence, so it's necessary to do two things: ...
6 votes
1 answer

Secondary structure information at each frame in a VMD trajectory

I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list to calculate the secondary structure ...
54 votes
3 answers

DeepMind just announced a breakthrough in protein folding, what are the consequences?

There was some recent media reporting about a purported Google breakthrough on applying machine learning techniques to tackle the protein folding problem, as told for example in this news article, ...
18 votes
1 answer

Does DeepMind's new protein folding software (AlphaFold) also work well for metalloproteins (proteins with metal cofactors)?

(1) Commonly, the metal is at the active site which needs the most prediction precision. (2) Typically, there is only one (or a few) metals in a protein, which contains far more other atoms. So, the ...