57 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 ...
Nike Dattani - No Free Time's user avatar
18 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 ...
epalos's user avatar
  • 4,789
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
  • 4,741
10 votes
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Where to find DNA structural atomic coordinates?

If you know the program AMBER, There is an option where you write an input with the sequence that you want, automatically the program will build the two strands, and your output will be pdb format. Or ...
Abd-Elazeem Mohamed's user avatar
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
  • 3,953
6 votes
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What software is a software for RNA tertiary structure prediction?

Rosetta The protein modeling program Rosetta includes RNA structure prediction functionality. I think the most up-to-date tool is the FARFAR2 protocol. You can try it out through the Rosie FARFAR2 ...
WaterMolecule's user avatar
6 votes
Accepted

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 ...
WaterMolecule's user avatar
5 votes
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An algorithm for implicit bond order and charge allocation for atomic coordinates?

This can be achieved by a 2-step process: Step 1: Convert XYZ to SDF using this open source python library xyz2mol Step 2: Use the SDF to get the bond order and formal charge information using Python +...
Vandan Revanur's user avatar
5 votes
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Force field for charged peptide-ion system

If you are looking at the interactions between a charged peptide and ions, I would recommend that you look into polarizable FFs that are available in literature. I know that OPLS and CHARMM have ...
Hemanth Haridas's user avatar
5 votes

How to show orientation axis in Pymol

As far as I know, there is no built in way to display the coordinate vectors. Fortunately, on the PyMOLWiki I was able to find a page with a number of scripts you can use to do this.
AwakenYesterday's user avatar
5 votes

Why are condensed matter predictions considered on par with experiment, while structural biology modeling receives more skepticism?

If this is happening, I think there's a few reasons: Quantum physics in general is the science subject where the most precise agreement between theory and experiment exists. For example, the ...
Nike Dattani - No Free Time's user avatar
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
  • 1,800
4 votes

How are diffusion coefficients calculated?

I decided to make my comment an answer... Diffusion coefficients are simple to calculate in molecular dynamics. GROMACS has built in software specifically for this calculation. GROMACS diffusion ...
B. Kelly's user avatar
  • 4,366
3 votes

An algorithm for implicit bond order and charge allocation for atomic coordinates?

This depends on your workflow purpose. It is usually straightforward to draw chemically sensible bonds between atoms -- this can be done in VMD using Topotools, as one example -- but partial charges ...
Shern Ren Tee's user avatar
3 votes
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What software can do RNA secondary structure prediction?

In the Wikipedia link you provided, there are several packages capable to predict the RNA secondary structure already including pseudoknot prediction. Also, the links to the source code, executable or ...
Camps's user avatar
  • 23.3k
3 votes

Where to find DNA structural atomic coordinates?

For batch use, I recommend Open Babel which can translate fasta format DNA sequences into single or double-stranded DNA coordinates. (Indeed, it's used in Avogadro.)...
Geoff Hutchison's user avatar
2 votes

Domain decomposition error while applying bonded restraints - GROMACS

The answer is not the actual solution to the error posted but a workaround. This is what I learned from the GROMACS mailing list: There is a minimum cell length for each domain decomposition cell in ...
Vasista's user avatar
  • 1,291
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
  • 23.3k
2 votes

Non-Covalent Interaction between drug and DNA?

Since it has been a month since OP agreed to write an answer without actually writing the answer, I will try answering this. The easiest way is to perform something called Enhanced Sampling ...
Hemanth Haridas's user avatar
2 votes

How to control the thickness of lipid bilayer with GROMACS

You can adjust the thickness of the water layer* by initialising your simulation with more or less water in it. The thickness of the lipid bilayer is determined by the types of lipids you use, and the ...
Shern Ren Tee's user avatar
2 votes

How to show orientation axis in Pymol

The supplied answer is correct, but is script and I (a passerby, not OP or responder) wanted a copypaste in the GUI. To make the code okay for copy pasting (i.e. no multilines): ...
Matteo Ferla's user avatar
1 vote

Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

Thanks for updating the question PriZarah, I can now at least suggest what might be causing the problem. It's probably just very, very slow In your recent example, you are calculating a reasonably ...
leeman's user avatar
  • 246
1 vote
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What is the purpose of DSSP when using martinize2?

Just basically collecting the comments here. The tutorials page for Martini states: The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters ...

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