56 votes
Accepted

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 ...
user avatar
17 votes
Accepted

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 ...
user avatar
16 votes
Accepted

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 ...
user avatar
14 votes
Accepted

How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here: The main issue are the units. The input parameters for reax force fields ...
user avatar
  • 1,341
12 votes

How to calculate the computational time required for a MD simulation

The simulation speed and efficiency depends on the hardware and software that you use. Things that you should keep in mind are, Every computer is unique in its ability. So only someone with access to ...
user avatar
  • 2,454
11 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 ...
user avatar
  • 4,153
11 votes

What are the factors to consider before docking 2 proteins?

The main requirement is to have structures files with good resolution. According to RSCB PDB documentation: Resolution is a measure of the quality of the data that has been collected on the crystal ...
user avatar
  • 18.7k
9 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 ...
user avatar
9 votes

How to calculate the computational time required for a MD simulation

Short answer: Do a short test run for performance estimates. Once you're familiar with a specific hardware/software combination, you may be able to estimate based on the size of the system, but the ...
user avatar
  • 1,877
8 votes
Accepted

Chimera or other software to perform protonation states of a protein

H++ H++ is a web service that permits to protonate your macromolecules using using different pH conditions. From its site: H++ is an automated system that computes pK values of ionizable groups in ...
user avatar
  • 18.7k
8 votes

Which non-commercial software can be used to dock two proteins?

HADDOCK HADDOCK is both a web service and a standalone code. From the web server: HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the ...
user avatar
  • 18.7k
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 ...
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 ...
user avatar
  • 3,599
6 votes
Accepted

Finding conformations of peptide based on dihedral angles

I don't think that any classification of dihedral angles exists. α and β that you see in the picture refer to alpha helices and beta sheets – structural elements of proteins (secondary structure). ...
user avatar
  • 1,485
6 votes
Accepted

Dihedral angles of alanine dipeptide

Proteopedia suggests that the $\phi$ and $\psi$ angles of a Ramachandran plot only involve carbon and nitrogen atoms in their definition and specifically the carbons and nitrogens in the backbone of ...
user avatar
  • 14k
6 votes

How much of a difference in a protein's radius of gyration can be considered significant?

It depends on your actual scenario. If we assume that you have two Molecular Dynamics (MD) replicas for the same protein (and their respective trajectories), then when you perform a Radius of Gyration ...
user avatar
  • 879
6 votes

How to characterize surface features in proteins?

Normally, if various proteins have the "same" cavities/clefts, this means that they are part of the same family and the amino acids that form the cavity are conserved. I really don't think ...
user avatar
  • 18.7k
6 votes
Accepted

Calculating RMSF in VMD

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely ...
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 ...
user avatar
  • 1,409
6 votes
Accepted

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 (...
user avatar
  • 974
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 ...
user avatar
6 votes

How to extract specific frames/model from a multi model pdb file?

Do you have access to OpenBabel to run from the terminal? For the purpose of demonstration, the example following is demonstrated on a file listing SMILES strings. However, the concept may be applied ...
user avatar
  • 1,449
6 votes

Alternative to CGenFF for generating large ligand topology

I'd use OpenMM's openmmforcefields package, which is available on GitHub. I haven't used it extensively, but I recommended to a student in a colleague's lab and ...
user avatar
6 votes
Accepted

Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides

I'm not sure if it's improper to answer my own question, but I think I've cracked it. For each peptide bond match identified by GetSubstructMatches the index [1] is ...
user avatar
  • 111
6 votes

How are diffusion coefficients calculated?

There are several different methods to calculate diffusion coefficients depending on the problem and some nuances to consider. Mean square displacement The most common way to calculate diffusion ...
user avatar
5 votes

Can we assume that the intraceullular pH and intermembrane pH are the same when calculating the protonation state of a protein subunit?

Generally not. The pH difference between the two sides of a membrane can be very noticeable, for example when the membrane is that of a mitochondrion. Actually mitochondria works by actively ...
user avatar
  • 6,643
5 votes
Accepted

How are tertiary protein structures represented in computers?

You don't specify what the algorithms shall do. If represented does not equal to visualization, then a the structures may be stored, transferred and processed via the atomic coordinates of the ...
user avatar
  • 1,449
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 ...
user avatar
  • 1,409
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 ...
user avatar
  • 18.7k
5 votes

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

Not a full answer, and it's too big for as a comment, but I can explain the linefix charge all qeq/reax 1 0.0 10.0 1.0e-6 reax/c. This function uses the charge ...
user avatar
  • 331

Only top scored, non community-wiki answers of a minimum length are eligible