Todd Yeates has received The DeLano Award for Computational Biosciences

Todd Yeates has received The DeLano Award for Computational Biosciences by the American Society for Biochemistry and Molecular Biology (ASBMB). The Award is given in the field of computational biology for “the most accessible and innovative development or application of computer technology to enhance research in the life sciences at the molecular level.”

The prize was established in memory of Warren Lyford DeLano, who developed PyMOL, an open source molecular viewer software and was an advocate for open source practices in the sciences.

Previous winners of this prestigious award include Vijay Pande, Michael Levitt, Helen Berman, Barry Honig and Axel Brunger.

Todd is recognized for his multiple, profound contributions to computational biology. These include: methods to design large, open protein shells capable of encapsulating cargo; methods to infer protein interactions from genome sequences; a powerful method to detect errors in protein structures; and a method to detect twinning which often bedevils protein structure determination.

See this article at the UCLA Newsroom

An illustration of ‘diffusion accessibility’ (Tsai, Holton, and Yeates, Protein Sci. 2015 Jul 16) a computational method for characterizing the surface shapes and binding clefts of macromolecules, implemented and rendered in PyMol. []

UCLA-DOE Institute to support UCLA’s iGEM team (International Genetically Engineered Machines) in the 2015 annual competition in Boston.


The main program at the iGEM Foundation is the International Genetically Engineered Machine (iGEM) Competition. Click here for more information.

See the video made by the UCLA iGEM undergraduate team


Next APS Trip

October 21, 2015

UCLA-DOE researchers and their colleagues publish new ideas for redesigning photosynthesis to meet global food demand crisis.

See “Redesigning photosynthesis to sustainably meet global food and bioenergy demand” in PNAS vol. 112 no. 28


Next APS Trip

April 17th to the  20th (2015)

International collaboration co-led by Prof. David Eisenberg elucidates the mechanism of safe storage and action of the potent human toxin MBP-1

Eosinophils are white blood cells that are part of the body’s innate immune defense against pathogens. Once an infection occurs, eosinophils are activated and migrate to the infected tissue where they contribute to kill the invading microorganisms (bacteria, viruses or helminths) by secreting a number of toxic proteins, including the Major Basic Protein (MBP-1).
While eosinophils are typically maintained at very low numbers in blood, in certain diseases, such as allergies, bronchial asthma, eosinophilic esophagitis or other eosinophilic syndromes, a highly increased number of cells is present. In these diseases, eosinophils can be aberrantly activated and infiltrate organs where, by releasing MBP-1 and other toxins, they can generate substantial tissue damage.
The Eisenberg lab co-led an international collaboration of scientists from over 10 different institutions to elucidate the details of how the powerful MBP-1 toxin is safely stored inside the eosinophil cell as well as the mechanism of its toxicity upon extracellular release. The findings were published this month in Molecular Cell.

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Crowd Phasing

homepage_pickWe have a new CrowdPhasing game that we would like everyone to try to play. It was begun briefly as part of a conference demonstration last month, and it was a promising start, but now we need to play the game in earnest to see how far it can progress. This one is distinctly different from previous games. This one is based on a *racemic* crystal, which simplifies the phase problem by allowing only two possible choices for each reflection (as you probably know). So far the experience is that this racemic game is a bit easier to make work than previous ones.
As usual, the purpose of the game is to try to drive the phases and their corresponding electron density maps to the correct solution, which should look like a very low resolution boundary of the unknown molecule. In the present case, we take as known information only that the unit cell should contain two copies of a small/compact cyclic polypeptide, whose molecular envelope should be relatively simple in shape at low resolution. Please join and play the game in the usual way. The name of this game is “Racemic peptide: kB1”. The link to the Crowdphase site is here. If you run into technical problems, ask Julien for help (

Crowdsourcing the phase problem

Successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it possible to extract meaningful information in cases where limited resolution might otherwise prevent initial phasing.

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Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the α-carboxysome.

Nicole Wheatley in the Yeates lab recently received her Ph.D. degree after her success in discovering a RuBisCO chaperone, dubbed alpha-carboxysome RiBisCO assembly factor (acRAF). Carboxysomes are bacterial microcompartments that assist in the fixation of carbon dioxide from the atmosphere. RuBisCO is the enzyme that catalyzes the fixation, and is estimated to be the most abundant enzyme on earth.

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