Archive for the 'Bioengineering' Category

Dynameomics: Mass annotation of protein dynamics

Published
by
Adam
on April 23, 2008
in Bioengineering, Data Warehouse and Molecular Dynamics
. 0 Comments

Just in case you need another -omics in your biotech vocabulary. Dynameomics is an effort by the Dagget group at the University of Washington to

characterize the native-state dynamics and folding/unfolding pathways of representatives of all known protein folds by way of molecular dynamics simulations

Three successive articles have been published in Protein Engineering Design & Selection to describe over 3000 long molecular dynamics simulations, the computational workflow, and data mining capabilities of Dynameomics. Dynameomics has applets for visual analysis and even high-quality movies of their MD trajectories!

Papers:

Video: 4PGA unfolding movie

Biorobotics: Snake Robots! [Video]

Published
by
Adam
on March 7, 2008
in Bioengineering and Video
. 0 Comments


These things are being developed by the Robotics Institute on our campus. I’m partially amazed and partially terrified. I’ve heard they work wirelessly and they want to have snakes where each module has a camera so they can break apart into independent pieces, spread, and reassemble automatically. Some of the climbing behavior is pretty impressive…

Read more about this technology at the Modsnake website.

Protein Design is inverse Structure Prediction

Published
by
Adam
on March 22, 2007
in Bioengineering, Bioinformatics and Protein Design
. 0 Comments

If we imagine protein folding as the exploration by a human explorer navigating a rugged landscape in search of the lowest elevation point, then how do we describe protein design? If we are still baffled by structure prediction in the ‘midnight zone’ how can we have a bioengineering strategy that is worth the title ‘protein design’?

When does Bioinformatics become Bioengineering? Is protein design really just inverse structure prediction? Does that work to simplify the problem?

I have always looked at the problem from the perspective of predicting ternary structure from primary structure. It almost seems more practical to flip the problem around. Given a structure and function, can we predict the amino acid sequence?

DNA synthesizers are rapidly improving. We still do not understand how a change in the amino acid sequence affects changes in protein structure. Template based modeling is progressing, anything beyond a sequence identity of 30% can be reliably modeled with a good pipeline.

Reliable function prediction is obviously the next milestone, but I think the gap from structure to function is still enormous. How do we standardize function specification? Enzyme functions can be described by the reaction they catalyze or the pathway they are part of. However not all proteins are enzymes. And not all enzymes are proteins. Hormones, transcription factors, membrane receptors all have some characteristic structure that supports their function.

Function prediction needs about 10 years before it can provide the type of infrastructure for robust bioengineering and truly rational drug design.