Part number 7. RNAInSpace - software for semi-automatic RNA construction in space
In previous parts From proteins to RNA , Mat. criteria How to reduce the number of turns the chain? How to evaluate the course of folding of single-stranded RNA? , The limitation of optimizing methods in games with and without adversaries , One fundamental problem , Introduction to folding multi-coil RNAs I told the basics to the cybernetic-geometric approach I proposed for the task of folding RNA . I will repeat the statement of the problem:
We have an arbitrary, actually existing, primary sequence of up to 100 nucleotides. We know all the hydrogen bonds that need to be formed. At the output we get the file .pdb, in which the tertiary structure from the specified primary sequence and where all the required hydrogen bonds are formed.
Here I will talk about practice, so that everyone can try what it is. I developed software for calculating what I was talking about. Here I give a link to the demo version . And I explain what you can see. It's better to see once than to hear 100 times :)
')
After you download ( download from here ), unzip, and run RNAInSpace.exe, click "Start" to see the screen (only with an empty upper and lower window) (the existing bug is known, sometimes the upper window may not normally fall into place) just restart and repeat):
This is really a demo version, you can not control the folding algorithm. But otherwise, you can follow the folding. Initially, the version is configured to fold one helix of the T-loop of the transport RNA of the body Escherichia coli, which carries phenylalanine, below its secondary structure (the part that is labeled “T”):
Now how to manage the demo version.
The first thing you do after the download is to click on the “Start minimizing” button. Numbers will start to appear in the lower console screen. About them later. Check in the directory where RNAInSpace.exe is located, the X _ #. Pdb files began to appear. As soon as X_0.pdb appeared, click on the “Add molecule” button. On the screen above, you will see a strand of RNA elongated in line. You can click the "Select nucleotides" button. There will be 4 pairs of nucleotides that must form hydrogen bonds between each other (but they can be changed by entering the number of nucleotides above, after the word resid, which you want to display). The two Checkboxes below show / hide the hydrogen bonds (if any) and all the nucleotides of the chain.
As soon as the next X_1.pdb, X_2.pdb, X_3.pdb, etc. appears You can click the “Add the following position” button and see how the RNA starts to roll up a little.
Graphic window can be expanded. As well as controlling the mouse, you can rotate the molecule (press the left / right button and move it - it rotates, we turn the wheel to increase / decrease).
If you turn off the program and start it again, the folding will not start from the beginning, but from the last step on which the folding stopped last time. If you want to start from the beginning, you need to clear the traj.dat file. And in order not to get confused, the next time you start, you should delete all the old X _ #. Pdb and X _ #. Txt files. You can also view the .pdb format in standard molecular imaging software, such as PyMOL .
The demo version does not guarantee that the spiral will collapse - this is how lucky :)
As soon as you play around with the visual presentation and want to figure out what the numbers in the console mean (however, if you carefully read past articles, you can guess) during the calculations and what else can be done on the demo program, or just ask questions, in the next part I will try summarize the questions and make a FAQ. Of course, if required and there will be interest.
PS Maybe someone is unlucky, my graphics on the laptop do not load until I understand what the problem is. Write about your problems, as far as possible I will look.
upd. I am testing this demo program in parallel. At step 192 (file X_192.pdb) an interesting situation just appears, which I described in Part 5. One fundamental problem . There hydrogen bonds are formed between the ends of the helix (1-16 nucleotides) while inside the helix are not yet formed. Then they will tear and form at first closer to the loop.
We have an arbitrary, actually existing, primary sequence of up to 100 nucleotides. We know all the hydrogen bonds that need to be formed. At the output we get the file .pdb, in which the tertiary structure from the specified primary sequence and where all the required hydrogen bonds are formed.
Here I will talk about practice, so that everyone can try what it is. I developed software for calculating what I was talking about. Here I give a link to the demo version . And I explain what you can see. It's better to see once than to hear 100 times :)
')
After you download ( download from here ), unzip, and run RNAInSpace.exe, click "Start" to see the screen (only with an empty upper and lower window) (the existing bug is known, sometimes the upper window may not normally fall into place) just restart and repeat):
This is really a demo version, you can not control the folding algorithm. But otherwise, you can follow the folding. Initially, the version is configured to fold one helix of the T-loop of the transport RNA of the body Escherichia coli, which carries phenylalanine, below its secondary structure (the part that is labeled “T”):
Now how to manage the demo version.
The first thing you do after the download is to click on the “Start minimizing” button. Numbers will start to appear in the lower console screen. About them later. Check in the directory where RNAInSpace.exe is located, the X _ #. Pdb files began to appear. As soon as X_0.pdb appeared, click on the “Add molecule” button. On the screen above, you will see a strand of RNA elongated in line. You can click the "Select nucleotides" button. There will be 4 pairs of nucleotides that must form hydrogen bonds between each other (but they can be changed by entering the number of nucleotides above, after the word resid, which you want to display). The two Checkboxes below show / hide the hydrogen bonds (if any) and all the nucleotides of the chain.
As soon as the next X_1.pdb, X_2.pdb, X_3.pdb, etc. appears You can click the “Add the following position” button and see how the RNA starts to roll up a little.
Graphic window can be expanded. As well as controlling the mouse, you can rotate the molecule (press the left / right button and move it - it rotates, we turn the wheel to increase / decrease).
If you turn off the program and start it again, the folding will not start from the beginning, but from the last step on which the folding stopped last time. If you want to start from the beginning, you need to clear the traj.dat file. And in order not to get confused, the next time you start, you should delete all the old X _ #. Pdb and X _ #. Txt files. You can also view the .pdb format in standard molecular imaging software, such as PyMOL .
The demo version does not guarantee that the spiral will collapse - this is how lucky :)
As soon as you play around with the visual presentation and want to figure out what the numbers in the console mean (however, if you carefully read past articles, you can guess) during the calculations and what else can be done on the demo program, or just ask questions, in the next part I will try summarize the questions and make a FAQ. Of course, if required and there will be interest.
PS Maybe someone is unlucky, my graphics on the laptop do not load until I understand what the problem is. Write about your problems, as far as possible I will look.
upd. I am testing this demo program in parallel. At step 192 (file X_192.pdb) an interesting situation just appears, which I described in Part 5. One fundamental problem . There hydrogen bonds are formed between the ends of the helix (1-16 nucleotides) while inside the helix are not yet formed. Then they will tear and form at first closer to the loop.
Source: https://habr.com/ru/post/141076/
All Articles