Re: [DIYbio] Re: Medicine Simulation Newbie

I think your question is a complicated one. What do you mean by accuracy?

People have "accurately" folded small proteins using simulations as measured by the Root Mean Square Deviation(RMSD) between the backbone(C alpha I think) of the two structures. But still, what do you mean by accurate? A 1 angstrom RMSD? A 0.5 angstrom RMSD? &c. How long.often does the simulation need to sample that state before you view it as significant? 5 picoseconds? 100 picoseconds?

Protein function is a thermodynamic problem. There really is no measure of "accuracy". Proteins are constantly being altered by their environment(i.e. temperature and solvent) see work by Boltzmann and Gibbs to start. What this means is that there are a very high number of possible conformations a protein can undertake. We call this the ensemble. Theoretically an ensemble contains every possible conformation of the protein. Most physical measurements we do of proteins are ensemble measurements. A Molecular Dynamics simulation is a single molecule equilibrium simulation which can't possibly sample all known states of the protein. For a single small protein with 100 amino acids and 3 degrees of freedom for each backbone phi psi angle you are talking 3^198 (This doesn't include sidechains and is probably a gross underestimate) see http://en.wikipedia.org/wiki/Levinthal%27s_paradox. There are techniques to increase the sampling frequency of different states but 3^198 is an awful lot. Your CPU clock frequency is probably 3^9 / second which means is would take about 9^86 years just to count that high without doing any other calculations.

I think the question you might be trying to ask is "Can simulations predict protein function or binding to other molecules?" The answer to that is "Sometimes". It really depends on the thermodynamics of the protein in question and the difficulty in sampling the state you are attempting to understand.

I don't know what you mean by "different environments". Different solvents? With other molecules? In a membrane? All of the above?

Josiah Zayner

On Thu, Nov 27, 2014 at 11:47 AM, Ujjwal Thaakar <ujjwalthaakar@gmail.com> wrote:

To what level of simulation accuracy has computational biology reached? To what degree of accuracy can we predict the behaviour of molecules in different environments?

On Wednesday, November 26, 2014 4:56:47 AM UTC+5:30, Josiah Zayner wrote:

I think first you need to understand some basic biochemistry before you begin.
Unless you are trying to simulate disease spread. Numerous people have worked on this and articles and methods should be easy to find.

If you are trying to understand how drugs help prevent or cure diseases such as Ebola you need to look at the proteins. Here is a tutorial for that: https://docs.google.com/document/d/13H-d8TzDn3m1H2BE_RA617H7g7dBjz_yibCLhLDejSQ/
which can be followed up with simulating the proteins which can be achieved with a tutorial like this: http://web.mit.edu/vmd_v1.9.1/namd-tutorial-unix.pdf


On Tuesday, November 25, 2014 5:58:38 AM UTC-8, Gokula Krishna wrote:

Hello There,

I am a Computer Science Engineer who is interested in simulating vaccines for various disease. Can anyone help me out on how to proceed? I have searched for various journals regarding this, but it is subtle to grasp and they are too abstract. 

This is the basic thesis that I have regarding the program:

1-> The user should specify the disease the various properties about the disease and environment.

2-> The program tests whether the given disease is curable for the vaccine.

3-> What are the parameters should I consider?

Can you suggest me a good place to start with?

Thanks in advance.

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