5 replies [Last post]
Joined: 02/24/2011
Groups: None


Elevator pitch summary: View and manipulate energy so geometry becomes a side-effect.

The game is beautifully executed and ingenious. And frustrating but that is just a side-effect of reality. As I explore this system, I wonder about something. I am reaching here and it may be a dead end but might be worth thinking about. Also it may seem interesting to me just because I am ignorant.

The entire picture is built around spatial representation of the proteins. But the spatial realization of the energy state of the protein is just a side-effect of its energy state. This spatial bias also affects the methods of control and manipulation. Its drawback becomes apparent when very small changes in the geometry result in very large swings in the score.

Is there a natural, sensible way of visualizing and manipulating the energy states of the protein, and segments of it and its environment? Like a potential field defined on the elements of the sequence. Like letting the 20th element of the chain see the field in the vicinity of the 43rd element. I hope that small changes in the energy in a certain part of the chain would, for the most part, lead to small changes in the overall state and that gradients in the potential field would become apparent as drivers of change.

Joined: 02/24/2011
Groups: None
Graphic tool


Elevator pitch summary: Graphic display of first and second derivative(difference) of the score function.

I find the derivatives of the score function very helpful but it would be nice to monitor them directly.

phi16's picture
User offline. Last seen 2 hours 51 min ago. Offline
Joined: 12/23/2008
View and manipulate energy

Dane2010, I've thought about this same subject many times. You're absolutely correct. Since the depiction of the protein is a graphical representation of three-dimensional space, it is easy to understand the relationship of distance to force. Since the effects of the push/pull of one atom on another are invisible, it is much more difficult to depict or understand.

I wonder if Fold.it, redesigned as a Wii type game might allow us to push/pull and 'feel' our way to better solutions?

Joined: 06/17/2010
VR gloves!!!

+ holographic projector : the only solution :)

Joined: 02/24/2011
Groups: None
thinking like a protein


Elevator pitch summary: Do proteins think in space or do they think in energy?

I keep thinking that spatial representation is misleading - not because it is irrelevant but because it is the effect not the cause. The cause is the evolution of the chain to a lower energy state.

Wiggle and shake are certain ways of "turning up the heat" to enable the chain to hop out of a local extrema well.

"Bands" seem to me very unphysical, perhaps just due to my ignorance.

Also I wonder why the "hydrophobic" "hydrophilic" characteristics might not be linked to a "hydro"-field that repels one and attracts the other. I have been using bands to turn hydrophobic's inward but I hear the chains screaming in pain when I do.

The sequence chain provides a natural finite set (space) to calculate energy on. That calculation I expect plays a rather significant role in calculating everything else form position to bonding to score. I wonder what patterns emerge when we look directly at energy representations, over the sequence, over pairs, over triplets, etc.. The cost of combinatorial explosion is mitigated to some extent but computing power. There is likely a point of diminishing returns that isn't too terribly huge. 1/r^2 is our friend.

This line of thought may be a been-there-done-that for the dev's, or too silly to be worth the trip. Maybe I just have a Hamiltonian analogy trapping my brain.

phi16's picture
User offline. Last seen 2 hours 51 min ago. Offline
Joined: 12/23/2008
Suggest alternatives

It might be time to take a leap into the unknown.

Programmers should attempt various new ways of representing forces at play then let the Fold.It community play with the representations. it might foster some further refinements by the community that produce good results.

Here's a few suggestions:

-- use translucent colors to represent energy. Overlapping energy fields, from the point of view of the observer, would appear stronger (deeper color).
-- use display of individual atoms where size equals strength
-- vibrate backbone and side chains according to their energy. the longer and faster the vibration, the stronger the energy attraction.
-- use black arrows with long shafts that start from the player's point of view and represent the strength of the energy forces by making the shaft thicker and the arrowhead larger. (If the idea is to give the player the ability to look around to see the relative forces in the neighborhood of an individual place on the protein)
-- Give players the ability to change the point of view of the player from outside the protein to inside the protein to a point of their choosing.

Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons