here - Biomedical Computation Review

NewsBytesInteractiveHandheld MoleculesThirty years ago, molecular biologistsroutinely constructed proteinmodels out of brass rods (“Kendrewmodels”). In recent years, researchersput away such tinker toys and turned tocomputer graphics.But now scientists at The ScrippsResearch Institute are combining thetwo mediums. They “print” threedimensionalmodels of biological moleculesthat, when held and manipulated,interact with the computer that printedthem. The work was published in theMarch issue of Structure.“Everyone has a gut feeling thatthere’s something different about holdingan object versus looking at it on thescreen,” says Art Olson, PhD, professorof molecular biology and director of theMolecular Graphics Laboratory at TheScripps Research Institute. “Butbecause these models are essentiallycomputer output, they have a specialrelationship to the data in the computerthat actually made them.”Olson and his colleagues generatehandheld molecules with 3D fabricatingprinters that can make solid objects outof layers of plaster or plastic. Then, as aperson turns or twists the object, a digitalvideo camera tracks its movements.The computer displays these manipulationsas well as additional informationabout the molecule in what is known as“augmented reality.” For example, as aperson moves two physical moleculestoward one another, the screen mightshow how the electrostatic fields andelectrical potentials change.Why bother with physical models atall? “If you can print out a custom interfacethat’seasy to handleand willaddress whateverproblemyou’re interested in, then why not try todo that?” Olson says. “You have moretools and more cues if you have the analogphysical object.”Physical models with augmentedreality have an advantage over purecomputer models because they’re moreeasily manipulated, Olson says. “It’seasy to tie a knot in a string with yourhands. It’s much harder on the screen.”“It’s easy to tie a knot in a stringwith your hands,” says Olson. “It’smuch harder on the screen.”Given a flexible model of a protein, aresearcher can pick apart the end terminusand see how it might interact iflain against a different part of itself.“Doing that with a mouse would be relativelydifficult.”Above: Computer augmentation of two subunits of the SODdimer which are tracked and manipulated independently. Theelectrostatic field is shown with small arrows that point alongthe local field vectors (they appear as small as dots in thispicture), and the potential is shown with volume renderedclouds, with positive in blue and negative in red. At Right: Aphysical ball and stick model of an amino acid is augmentedby computer graphics showing the spacefilling model superimposed.Courtesy of Art Olson, Molecular GraphicsLaboratory, The Scripps Research Institute.2 BIOMEDICAL COMPUTATION REVIEW Fall 2005 www.biomedicalcomputationreview.org