Developer Tales

Pipeline Dreams

Bridget Carragher and Clint Potter

Simons Electron Microscopy Center at the New York Structural Biology Center

Published April 26, 2016

A year ago, Bridget Carragher and Clint Potter’s group broke the so-called three-angstrom barrier for electron microscopy (EM). Prior to their work, so many structures had been solved using EM at 3.4 or 3.5-angstrom resolution that people had started to believe higher resolutions were out of reach with the technology.

"Our group set out to show that EM could do better,” says Carragher, co-Director of the Simons Electron Microscopy Center (SEMC) at the New York Structural Biology Center (NYSBC). “We did things carefully and in a fully automated fashion and got to 2.8 angstroms. That was …

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Computing Cellular Clockworks

Klaus Schulten

University of Illinois, Urbana-Champaign

Published October 23, 2015

Physicist Klaus Schulten once imagined becoming a dancer, relying on nothing but his own mind and body to perform. “But I was not a good dancer,” he says. “So my next thing was theoretical physicist. Just myself, pencil and paper — and in my case, also an eraser.”

That dream was also thwarted. Today, Schulten relies on some of the most powerful and expensive computing equipment on earth to carry out his work, which applies theoretical physics to the understanding of biological systems. His most recent work involved the molecular simulation of an organelle that converts …

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Into Alignment

Geoff Barton

Division of Computational Biology, University of Dundee

Published May 27, 2015

In 1987, when Geoff Barton was a graduate student learning computational structural biology at the University of London, just 6000 protein sequences were known, but their numbers were rising exponentially, and it was becoming clear that they had commonalities. Sequences that yield valuable functions have staying power, so they are conserved throughout evolution. Finding these recurring patterns, however, required painstaking pencil and paper comparisons.

A page from Barton's lab book in around 1988. It shows a multiple sequence alignment produced automatically by his alignment software, printed out then coloured by hand to highlight conserved amino acid …

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Wire Models, Wired

A brief history of UCSF Chimera

Published October 29, 2014

The molecular graphics software called Chimera, written and supported by a team of scientists in Tom Ferrin’s lab at the University of California, San Francisco (UCSF), has been cited over 7000 times and helps biologists and drug developers visualize molecules and biological structures in 3D at various resolutions. The tool has a personal history that traces back to 1994, and an ancestral history that stretches nearly four full decades earlier, to a London lab in 1955 and a man named Robert Langridge, also known as the pioneer of molecular graphics.

^{Bob Langridge. Photo by Christopher Springmann, …}

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