Hello. I'm new here, and I've just finished the basic tutorials. I am not a biochem student, so forgive me if my questions are essentially noob :)

Why is better to crowd source different ways to fold rather than simply write algorithms to consider every possible fold (given a certain number of nucleotides to start with) and evaluate each fold? One obvious answer is that if the number of nucleotides are many to star with, the number of possible permutations of folds go up exponentially. But then, automated ways are efficient at just this sort of thing, yes?

And thirdly, the energy counter on the top left corner, is the idea to keep this as low as possible. I am assuming that this is the energy it takes to 'mutate' one nucleotide to another, and thus any stable fold achieved using a minimum of energy expenditure is a 'better' design. Is the negative sign simply an indication that it represents energy 'consumed'?

And thirdly, is it a given that a certain distribution of nucleotides always results in a certain 'folding'? Does the game abstract out other parameters?

And lastly is there any write up that gives whys and the hows of folding RNAs. This could probably answer most of my questions above.

Why is better to crowd source different ways to fold rather than simply write algorithms to consider every possible fold (given a certain number of nucleotides to start with) and evaluate each fold? One obvious answer is that if the number of nucleotides are many to star with, the number of possible permutations of folds go up exponentially. But then, automated ways are efficient at just this sort of thing, yes?

And thirdly, the energy counter on the top left corner, is the idea to keep this as low as possible. I am assuming that this is the energy it takes to 'mutate' one nucleotide to another, and thus any stable fold achieved using a minimum of energy expenditure is a 'better' design. Is the negative sign simply an indication that it represents energy 'consumed'?

And thirdly, is it a given that a certain distribution of nucleotides always results in a certain 'folding'? Does the game abstract out other parameters?

And lastly is there any write up that gives whys and the hows of folding RNAs. This could probably answer most of my questions above.

Allison McElfresh

alan.robot

So if you design a target where you use the same base-pair pattern over and over, you can be sure there will be suboptimal folds that show up in real life unless you add some randomness into it. Hopefully at some point the game will give you some sort of warning in these scenarios, until then just remember that lower free energy does not necessarily mean better.