Nav: Home

SLU scientist helps move structural biology into 'big data' era

March 15, 2016

ST. LOUIS -- In a recent paper published in Nature Communications, structural biologists detailed how a new data sharing consortium is helping scientists more quickly share and benefit from findings in their field.

Enrico Di Cera, M.D., chair of biochemistry and molecular biology at Saint Louis University, is an author on the paper and says that the Structural Biology Grid Consortium has developed a repository, the Structural Biology Data Grid, to deposit, search and download structural biology data sets. In the current study, researchers found that the repository was effective in allowing researchers to reproduce earlier findings, letting work in the field progress.

"This is a transformative development in the field," said Di Cera. "Finally, we may take full advantage of the enormous amounts of data being generated by structural biologists."

X-ray crystallography, one of the most powerful tools in structural biology, allows researchers to determine the structure of proteins, nucleic acids and other small molecules at atomic level resolution. Understanding a protein's structure opens the door to understanding the molecular basis of diseases and developing new therapeutic strategies of intervention.

Crystallographers share their findings in academic journals and currently use standard repositories of processed datasets like the Protein Data Bank. The Structural Biology Data Grid supports archiving of raw experimental datasets using a distribution model of computing clusters. Benefits include rapid access of the original experimental data for general use and validation. With the data collection process becoming increasingly streamlined, archiving through the Structural Biology Data Grid will become mainstream.

In order to better leverage the breakthrough findings coming out of laboratories around the world, structural biologists created the Structural Biology Grid Consortium. The consortium's strategies include: curating and supporting a collection of data processing software; managing raw, experimental data sets; establishing a publication system for data sets; and integrating the storage resources of multiple research groups and institutions.

In the current study, researchers conducted a pilot study, analyzing data from the repository collection. They found that the repository was effective in allowing researchers to reprocess data from earlier experiments, offering the opportunity to reproduce earlier findings, improve existing models, and catch possible mistakes earlier.

"The Grid started as a joint effort of top structural biology labs around the world. We are proud to be part of a great initiative that uses big data for the benefits of the entire scientific community," said Di Cera.
-end-
Enrico Di Cera, M.D., is the Alice A. Doisy professor and chairman of the department of biochemistry and molecular biology at Saint Louis University. He has devoted many years to the study of blood-clotting, a life-saving biological process that prevents excessive bleeding after injury, but which also has the potential to cause harm when triggered in the wrong conditions, as with deep vein thrombosis. Distinguishing himself throughout his career as a biophysicist, biochemist, structural biologist and protein engineer, Di Cera recently succeeded in crystalizing the key coagulation factor prothrombin -- a feat that had eluded scientists for four decades.

Established in 1836, Saint Louis University School of Medicine has the distinction of awarding the first medical degree west of the Mississippi River. The school educates physicians and biomedical scientists, conducts medical research, and provides health care on a local, national and international level. Research at the school seeks new cures and treatments in five key areas: cancer, liver disease, heart/lung disease, aging and brain disease, and infectious diseases.

Saint Louis University

Related Molecular Biology Articles:

Cell biology: All in a flash!
Scientists of Ludwig-Maximilians-Universitaet (LMU) in Munich have developed a tool to eliminate essential proteins from cells with a flash of light.
A biology boost
Assistance during the first years of a biology major leads to higher retention of first-generation students.
Scientists find biology's optimal 'molecular alphabet' may be preordained
Life uses 20 coded amino acids (CAAs) to construct proteins.
Molecular biology: Phaser neatly arranges nucleosomes
LMU researchers have, for the first time, systematically determined the positioning of the packing units of the fruit fly genome, and discovered a new protein that defines their relationship to the DNA sequence.
Molecular virologist fights influenza at the molecular level
In research to improve influenza therapies against H7N9 and other influenza strains, Chad Petit and his University of Alabama at Birmingham colleagues have detailed the binding site and mechanism of inhibition for two small-molecule experimental inhibitors of influenza viruses.
The complicated biology of garlic
Researchers generally agree that garlic, used for thousands of years to treat human disease, can reduce the risk of developing certain kinds of cancers, cardiovascular disease, and type 2 diabetes.
Study suggests molecular imaging strategy for determining molecular classifications of NSCLC
Recent findings suggest a novel positron emission tomography (PET) imaging approach determining epidermal growth factor receptor (EGFR) mutation status for improved lung cancer patient management.
The biology of color
Scientists are on a threshold of a new era of color science with regard to animals, according to a comprehensive review of the field by a multidisciplinary team of researchers led by professor Tim Caro at UC Davis.
Molecular microscopy illuminates molecular motor motion
A toddler running sometimes loses footing because both feet come off the ground at the same time.
Kinky biology
How and why proteins fold is a problem that has implications for protein design and therapeutics.
More Molecular Biology News and Molecular Biology Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Teaching For Better Humans 2.0
More than test scores or good grades–what do kids need for the future? This hour, TED speakers explore how to help children grow into better humans, both during and after this time of crisis. Guests include educators Richard Culatta and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#556 The Power of Friendship
It's 2020 and times are tough. Maybe some of us are learning about social distancing the hard way. Maybe we just are all a little anxious. No matter what, we could probably use a friend. But what is a friend, exactly? And why do we need them so much? This week host Bethany Brookshire speaks with Lydia Denworth, author of the new book "Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond". This episode is hosted by Bethany Brookshire, science writer from Science News.
Now Playing: Radiolab

Space
One of the most consistent questions we get at the show is from parents who want to know which episodes are kid-friendly and which aren't. So today, we're releasing a separate feed, Radiolab for Kids. To kick it off, we're rerunning an all-time favorite episode: Space. In the 60's, space exploration was an American obsession. This hour, we chart the path from romance to increasing cynicism. We begin with Ann Druyan, widow of Carl Sagan, with a story about the Voyager expedition, true love, and a golden record that travels through space. And astrophysicist Neil de Grasse Tyson explains the Coepernican Principle, and just how insignificant we are. Support Radiolab today at Radiolab.org/donate.