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

Imagine if given an amino acid sequence, you could quickly calculate what the shape of the corresponding protein would be. You would be able to predict what effect a mutation would have on the shape ...
Nike Dattani - No Free Time's user avatar
18 votes
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Introduction to protein folding for mathematicians

Great question! Protein folding has been in open question for decades. Just recently, there's been a lot of discussion regarding DeepMind's AlphaFold project, which was discussed at length on our very ...
epalos's user avatar
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17 votes
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Does DeepMind's new protein folding software (AlphaFold) also work well for metalloproteins (proteins with metal cofactors)?

It's a great question! Some of my answer will be taken from my answer to your question on the AI stack exchange, but cross-site questions are allowed and your question here is slightly different so my ...
Nike Dattani - No Free Time's user avatar
12 votes

Introduction to protein folding for mathematicians

Someone more familiar with the problem might have a better suggestion, but I recently came across Daniel B. Dix' notes on Mathematical Models of Protein Folding. This is not my field, so I won't ...
Anyon's user avatar
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10 votes

Introduction to protein folding for mathematicians

Preamble Since I don't know your specific background, this is a generic answer for any applied mathematician wishing to enter the field of protein folding. Not everything will apply specifically to ...
Nike Dattani - No Free Time's user avatar
7 votes

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

Keep in mind that many if not most proteins have multiple quasi-stable conformations, so their 3D structure is not actually a single conformation but rather a Markov matrix of conformations, with ...
Eric Minch's user avatar
7 votes

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

Probably one of the important applications is Computer Aided Drug Discovery (CADD). If the protein structure could be accurately predicted, one could design protein-ligand docking on the binding ...
Paulie Bao's user avatar
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6 votes

Secondary structure information at each frame in a VMD trajectory

I have found the solution to the problem. One needs to use the animate command to change the frame in the top molecule in VMD. The corrected script which produces ...
Roni Saiba's user avatar
6 votes

Protein structure prediction

I'm adding another answer because I recently find these news. The machine learning-based methods alphafold and rosettafold were recently released on github. Someone has just implemented it in Google ...
NickZ's user avatar
  • 1,489
6 votes
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Protein structure prediction

Here's what I did. Assuming that you have a part of the protein crystal structure. In my case, I have an incomplete structure of the protein. Lets say if I have an amino acid (AA) sequence of 520 (...
Vasista's user avatar
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5 votes

Protein structure prediction

In the past I had the same question and after a long search I found that every two year there is a worldwide competition to assess the quality of 3D structure prediction of proteins. In the past the ...
NickZ's user avatar
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5 votes

Protein structure prediction

Your protocol is right and rigorous in the sense as if you don't have the crystal structure of your protein and want to do some predictions, them the only way is using homology modeling. I am not a ...
Camps's user avatar
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5 votes

Restrain a protein to be helical in an MD simulation

Applying restraints to keep a specific secondary structure is common/mandatory when using coarse grained force fields for MD simulations, try searching for simulations with the MARTINI force field.
Frank Jensen's user avatar
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4 votes

Introduction to protein folding for mathematicians

I'd start from An Introduction to Protein Structure Prediction which is part of a just published course Biological Modeling: A Free Online Course. The author of this course is also a mathematician by ...
marcin's user avatar
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4 votes
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Restrain a protein to be helical in an MD simulation

The general method is to constrain the CA atoms of the protein while you are equilibrating the structure. You can do this in gromacs by creating a posres.itp file that has all the CA atoms, and then ...
Hemanth Haridas's user avatar
2 votes

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

In order to run Molecular Dynamics simulations (independent of the force-field and type of simulation) you need a file with the structure of your protein: type of atoms, residues and (X, Y, Z) ...
Camps's user avatar
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