# Tag Info

16

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 answer is slightly different. I'll address your points in reverse chronological order: (4) Most proteins don't have metals at all. It was estimated in 1999 ...

16

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 own site here. My answer will be complementary to the one above, but the references I will provide will be closer to the physics side of the problem. First ...

12

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 the exact same hardware (processor, gpu etc.) can test this out and tell you. As far as I know, there is no established method of calculating the computational ...

10

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 guarantee correctness. However, to a layman at least, these notes seem well suited for someone with your background. The abstract reads We present an elementary ...

9

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 general advice (especially with hardware you're not familiar with) is to do a short benchmarking run. Gromacs-specific practical advice: Use the -maxh option to ...

8

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 macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed ...

7

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 you, and please don't feel offended if there's something I assume you don't already know or do! First of all, as a fellow mathematician (I was trained in ...

6

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 match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...

6

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 probabilities of a given conformation and probabilities of transition from each conformation to its neighbors varying according to temperature, pH, and other ...

6

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 pockets and run molecule dynamics simulations. In the lead identification process of a CADD, the starting point is normally be the experimental data for the crystal ...

6

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 (full length), I have the pdb for certain domains which are functionally important. So, I went for homology modelling. I used two predictors Robetta and tr-Rosetta. ...

6

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 winner was an online services called I-tasser that you can find here. I tested it also in the past year with the covid spike protein and after the publication of ...

6

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 the desired output is as follows: set outfile [open ./percent_helix.dat w] set lookup {H G I} set frame_num [molinfo top get numframes] set full [atomselect top "name CA"] set len [...

6

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 on a .pdb with multiple models (and equally works well enough on multi-model .sdf). The input file input.smi is a small set of aromatics. SMILES strings and ...

5

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 protein. For proteins, the .pdb format is quite common. After a header, the (x,y,z) are described in a block like ATOM 1 N PRO A 1 8.316 21.206 21....

5

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 colab as Jupiter notebook that you can simply reuse with your colab account. The only thing that you need to do is change the AA sequence. It seems that in the ...

5

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 transporting protons from one side of the membrane to the other side, using the chemical energy released by reducing O2 to H2O, and then use the proton gradient to ...

5

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 big fan of homology modeling, so I always recommend to avoid it as possible. My addition will be that, instead using only one resource to model the 3D structure, ...

4

The main issue here is not about the type of ligands (glycans) even when it is known that there are force fields that are specific for each type of system. The main issue is about how flexible and big is the ligand you are using to dock. The GLIDE software, for example, has been increasing the number of atoms and rotatable bonds it is able to handle. Since ...

4

In a molecular docking, the affinity between a protein and a ligand is determined using what is called score functions. Each docking software has its own score function. These score functions are created/modified by the software developers and, in principle, they are not interchangeable: you can not compare two docking studies made with different docking ...

4

file=test.pdb #pdb file frame=10 # frame number to extract x_frame=$(egrep "MODEL.*$frame$"$file) sed -n "/$x_frame/,/ENDMDL/p"$file > ${file::-4}_frame_$frame.pdb output file will be written as filename_frame_10.pdb The bash script below provides easier (repeated) access to the functionality described: #!/bin/bash # Extract a specific .pdb ...

3

You can use the Python script multiple_model_PDB_file_splitter: # multiple_model_PDB_file_splitter.py by Wayne Decatur # ver 0.2 # #******************************************************************************* ## PURPOSE: Takes a formatted pdb file with multiple models and splits each model # into individual files. Requires the PDB file include both MODEL ...

2

Your approaches looks correct. Normally, the docking are done in physiological pH, so, only one pH. Maybe this is why you didn't see any works doing what you are trying ti do. But hey, this it is a good thing: you will be the first. My only recommendation is to carry all the calculations using the same protocol: same software, same protonation method, etc.

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