NBCR - National Biomedical Computation Resource was founded in 1994 to facilitate interaction among biomedical scientists and promote the development of computing power at the national supercomputer centers. Since that time, NBCR has led the development of new technology in computing to benefit the biomedical research community and bridge the gap between emerging information technologies and NIH-funded science across diverse biomedical research areas.

NBCR’s vision centers on the development of tools and technologies that enable models to bridge across diverse scales of biological organization that ranges from molecules to organs systems to gain a quantitative understanding of biological function and phenotypes, while enabling biomedical science to take full advantage of all types and sources of relevant data. Our products raise from our Driving Biomedical Projects, and is applied to a board scientific community. 

Click here for the list of NBCR Software, WebServices, Workflows, and Software Rolls

Research Highlights

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Visualizing Biological Specimens at Nanometer Scale Using a New Automated, More Detailed Method

The ability to locate and visualize proteins and macromolecular complexes in cells and tissues in 3D high resolution continues to be a challenge in biomedical studies. Various techniques and tools are key to this work. For example, light microscopy uses fluorescent labels to track elements of interest, but it provides an incomplete view, including only the distribution of the labeled elements. Researchers who want to collect more comprehensive 3D datasets at higher-resolution use electron microscopic tomography (EMT) to visualize all structures in the cellular or subcellular domain under investigation.

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Allostery and Protein Dynamics Across Scales

There’s long been a standard tradeoff in biochemistry: You can study overall shape (of, say, a macromolecule or an organelle) or high-resolution detail within, say, at the 10-40-nanometer scale. Seeing both at the same time would be one of today’s scientific Holy Grails.

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Biomedical Big Data Training Collaborative

For the last 5-10 years, a lot has been said and written about “big data” and the insight it’s reputed to hold – if only you can find an efficient, effective way to get at it. But big data can be a bewildering topic, as there seem to be as many types and formats of big data as there are methods to analyze it.

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Multi-scale Simulations with Applications for Drug Design

Lane Votapka, relaxed from a recent successful defense of his PhD research, sets the stage for the work he published this fall with his advisor and NBCR Director Rommie Amaro at UC San Diego: “The cell is made up of proteins and other large molecules. 

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cellPACK – a new tool to build complex systems

In collaboration with QB3 Fellow Graham Johnson at UCSF, NBCR investigators Art Olson and Michel Sanner have developed cellPACK, a new software tool to build increasingly complex systems.

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cAMP Binding Causes Protein Kinase Activation

In spite of several decades of research, scientists have been unable to describe in rigorous quantitative terms the exact sequence of events that leads to activation of Protein Kinase A (PKA) by cyclic adenosine monophosphate (cAMP). But a research team at UCSD will soon publish results that explain this mechanism for a PKA isoform essential for proper functioning of the heart.

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Experimentation and Computation Meet

A normal heart uses the complementary, alternating activities of “systolic” contraction and “diastolic” relaxation to pump blood throughout the body. So scientists are eager to understand the various factors that affect this process, including those that lead to heart disease and failure.

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Finding New Anti-Flu Compounds

By comparison with his peers, Eric Chen might be considered a veteran researcher. Currently a senior at Canyon Crest High School in northern San Diego County, he has already worked for two years in several laboratories – both computational and bench science – at UCSD and The Scripps Research Institute.

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Ilkay Altintas: Advancing Computational Research with Scientific Workflows

It was a lark that brought Ilkay Altintas to San Diego. The year was 2001. She had just finished her M.S. thesis and was working at the Middle East Technical University in Ankara, Turkey, when she discovered an open position at the San Diego Supercomputer Center (SDSC). 

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New Molecular Dynamics Method

A team of NBCR researchers recently demonstrated a new accelerated molecular dynamics (aMD) implementation that enhances sampling of the conformational space of biomolecules by several orders of magnitude. More specifically, they developed an implementation of the aMD method using the OpenMM toolkit library to produce high performance – and, as a result, longer simulation times – on graphics processing units (GPUs). 

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Nucleotide Diffusion in the Cardiac Myofilament Lattice

An NBCR research team recently published a paper investigating the spatiotemporal diffusion of adenine di- and triphosphate (ADP and ATP) nucleotides through the myofilament lattice in heart muscle. The investigation of diffusion of these biomolecules is important because they regulate cardiac energetics and coupling between cell excitation and contraction.

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Accelerated Molecular Dynamics Simulations

Using just an upgraded desktop computer equipped with a relatively inexpensive graphics processing card, a team of computer scientists and biochemists at the University of California, San Diego, has developed advanced GPU accelerated software and demonstrated for the first time that this approach can sample biological events that occur on the millisecond timescale. 

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Calcium Sparks Generation

Triggered release of Ca2+ from an individual sarcoplasmic reticulum (SR) Ca(2+) release unit (CRU) is the fundamental event of cardiac excitation-contraction coupling, and spontaneous release events (sparks) are the major contributor to diastolic Ca(2+) leak in cardiomyocytes. Previous model studies have predicted that the duration and magnitude of the spark is determined by the local CRU geometry, as well as the localization and density of Ca(2+) handling proteins. 

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Intracellular Calcium Dynamics Model

According to the Centers for Disease Control and Prevention (CDC), heart diseases are the number one cause of death in the US. Heart attacks are caused by blockages in coronary arteries, and heart failures or in severe cases, cardiac arrest, are often caused by irregular heart beats or arrhythmias.

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Myosin light chain kinase dephosphorylation

Actin-myosin interactions provide the driving force underlying each heartbeat. The current view is that actin-bound regulatory proteins play a dominant role in the activation of calcium-dependent cardiac muscle contraction. 

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New drug effective against MRSA

Millions of people die each year from bacterial infections in tuberculosis or pneumonia. The bacterium, Staphlococcus aureus, while usually harmless, may lead to ear infection, sinusitis, pneumonia, meningitis, toxic shock syndrome and a number of postsurgical infections.

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Pocket Full of Promise

Cancer remains the second leading cause of death, after heart diseases, in the US, and millions of people die from different types of cancer worldwide each year. The known tumor suppressor protein p53 is an important regulator of cell growth in normal cells and its dysfunction is closely related to tumor development and progression.

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Versatile Python API

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. 

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Active Conformational States

Lauded by Biomedical Research Community , the relaxed complex scheme (RCS) is a promising computational method for computer-aided drug discovery (CADD) that combines the advantages of docking algorithms with the dynamic structural information provided by molecular dynamics (MD) simulations.

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Attacking Chagas Disease

Projects in Scientific Computing publishes an article describing Studies with Anton, a special-purpose supercomputer designed by D. E. Shaw Research and made available at PSC, that have yielded new insights into the motion and function of proteins.

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Better Understanding of Heart Failure

Modeling Calcium Dynamics in Ventricular Myocytes with Realistic Transverse Tubules/em> What is known as cardiac remodeling (or ventricular remodeling) is not a good thing; it implies that there is a decline in the function of the heart. 

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Biomolecular Electrostatics

Scientists use a number of tools to investigate how cells develop, operate, communicate, and control their activities. Molecular interactions have several components, including biomolecular electrostatics, which is considered to be of special importance because of its long range nature and influence on polar or charged molecules (primary components in living systems).

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Major Step in Heart Modeling

A “picture” of your failing heart is worth a thousand words. The development and clinical use of patient-specific models of the heart is now a possible goal. Models have the potential to help with diagnosis and support decision-making for cardiologists and their patients. Several research groups are now working to develop multiscale models of the heart; these models integrate the many physiological functions taking place in the heart. 

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Tool Speed up for Computer-aided Drug Discovery

Found to be an efficient approach Drug discovery and design involves finding small molecules that are complementary in shape and charge to the biomolecular target with which they interact so that they will bind to it. Applying computational power to the combined chemical and biological aspects of this process is an ever-growing effort because doing so improves the speed of the process and development of effective treatments.

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Visualization and Modeling Integration

Bringing modeling and animation into one interface and improving interdisciplinary collaborations: Increasingly complex research has made it more difficult to prepare data for analysis, publication, education, and outreach. Many scientists must also wade through what seems like black-boxes with mysterious code that works “magic” to generate results with computational algorithms from diverse sources in order to supplement their laboratory (bench) work.

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Latest News

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C&EN talks with Rommie Amaro, computational chemist: Amaro discusses how she uses molecular dynamics simulations to find new cancer drug leads

Determining the structures of enzymes and other biomolecules with X-ray crystallography has deepened biologists’ understanding of the inner workings of cells and led to the design of many important drugs. Increasingly, researchers are using computer modeling to attain a more realistic picture of the movement of these biomolecules in their natural environment. Rommie E. Amaro, a professor of chemistry and biochemistry at the University of California, San Diego (UCSD), uses computational techniques to predict how enzymes regularly shift their configurations, revealing potential vulnerable areas for drug targeting. C&EN talked with Amaro about how she’s using dynamic models of enzymes to develop a new class of cancer drugs, work that is being commercialized by Actavalon, a San Diego start-up Amaro cofounded. Link to the full article from the American Chemical Society

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Using data science to return people to the labor force: New center at Computation Institute to unify labor, training, education and employment data

Despite persistent unemployment in the United States, millions of jobs are hard to fill due to a lack of qualified applicants. While community college and training organizations seek to equip people with the skills required for these openings, it’s a moving target as the American economy rapidly changes. Link to the full article from The University of Chicago

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TSRI Scientists Awarded $6.6 Million for Research in Computational Biology

Three groups at The Scripps Research Institute (TSRI) have been awarded grants from the National Institutes of Health (NIH) to develop methods for computational modeling and to apply them to cutting-edge systems in biology and health. “The three projects are highly symbiotic, each addressing a different state-of-the-art challenge in computational biology, but built using a common computational framework that will allow facile collaboration between the groups,” said Professor Arthur Olson, founder of the Molecular Graphics Laboratory, which is currently part of the TSRI Department of Integrative Structural and Computational Biology. Link to the full article from the Scripps Research Institute

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Supercomputing the P53 protein as a promising anticancer therapy

Even though it's almost impossible to see, computational biophysicist Rommie Amaro is using the Stampede supercomputer at the Texas Advanced Computing Center at The University of Texas at Austin to model the largest atomic level system of the tumor suppression protein p53 to date — over 1.5 million atoms. The simulations identify new "pockets" to reactivate p53 which would be a tremendous boost for future anti-cancer drug iscovery. Link to full article from Texas Advanced Computing Center

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This protein is mutated in half of all cancers. New drugs aim to fix it before it’s too late

It has been nearly impossible to get a good look at Rommie Amaro's favorite protein in action. Called p53, the protein sounds the alarm to kill cells with DNA damage and prevent them from becoming cancerous—one reason why it has been called the "guardian of the genome." But it is big and floppy, a molecular shapeshifter that is hard to follow with standard imaging tools. So Amaro, a computational biologist at the University of California (UC), San Diego, turned to supercomputers. Link to the full article from the American Association for the Advancement of Science

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Science at cusp of 'transformational' grasp of life via cell modeling, researchers say

A paper recently published in the Journal of Molecular Biology shows how advances in molecular biology and computer science around the world soon may lead to a three-dimensional computer model of a cell, the fundamental unit of life. According to the authors, the development could herald a new era for biological research, medical science, and human and animal health. Link to the full article from Phys.org

 

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La Jollan wins top prize in Theoretical Chemistry

J. Andrew McCammon, a distinguished professor of chemistry, biochemistry and pharmacology at UC San Diego, has won the 2016-17 Joseph O. Hirschfelder Prize in Theoretical Chemistry, awarded by the Theoretical Chemistry Institute at the University of Wisconsin-Madison. A physical chemist who is also a fellow of the San Diego Supercomputer Center and a Howard Hughes Medical Institute Investigator, McCammon is the second UCSD chemistry professor to receive the prestigious prize, following Peter Wolynes in 2009. Link to the full article from the La Jolla Light 

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Promising drug leads

Using a unique computational approach to rapidly sample, in millisecond time intervals, proteins in their natural state of gyrating, bobbing, and weaving, a research team from UC San Diego and Monash University in Australia has identified promising drug leads that may selectively combat heart disease, from arrhythmias to cardiac failure. Please see links to a Full article in UC San Diego News Center and a published paper.

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Andrew McCammon is 2016-17 Hirschfelder Prize Recipient

Professor J. Andrew McCammon will receive the 2016-17 Joseph O. Hirschfelder Prize in Theoretical Chemistry, administered by the University of Wisconsin-Madison Theoretical Chemistry Institute (TCI). McCammon is a professor of chemistry, biochemistry, and pharmacology at the University of California, San Diego, where he holds the Joseph E. Mayer Chair of Theoretical Chemistry. He also is a member of the National Academy of Sciences and a fellow of the American Association for the Advancement of Science and the American Academy of Arts and Sciences. Link to the full article from the University of Wisconsin-Madison Department of Chemistry.

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Report from the Summer School in Computational Physiology

17 students attended this year's Summer School, a joint venture in Computational Physiology between the University of Oslo, University of California, San Diego, and Simula. The Summer School is now in its third year, and including this year's group we have a total of 44 graduates from the school. This summer, 15 of the students were PhDs and two were Master's students, selected from a pool of international applicants. Link to the full article from simula

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Computing transforms chemistry, biotech

The life sciences are going dry. While test tubes, Petri dishes and cell cultures abound in the biotech world, the frontiers of exploration are increasingly taking place on high-powered computers and supercomputers. Equipped with ever better microprocessors to perform calculations and render graphics, computers today run extraordinarily powerful software that sheds light on biomedicine at every scale — from the physics of atomic-level interactions to sophisticated models of how tissues function. Link to the full article from the San Diego Union Tribune

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Computer Simulations Aid Search for “Resistance-Resistant” Antibiotics

With the growing threat of drug-resistant bacterial infections, new antibiotics are sorely needed. But we need truly novel classes of antibiotics, not just new versions that kill bacteria the same singular way existing drugs do, says J. Andrew McCammon, PhD, Distinguished Professor of Pharmacology, Chemistry and Biochemistry, and Joseph E. Mayer Chair of Theoretical Chemistry at UC San Diego. We need “resistance-resistant” antibiotics — drugs bacteria won’t easily be able to ignore. Link to the full article at News from UC San Diego Health Sciences. 

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The recipe for Big Data

What do a cookbook and big data have to do with each other? Quite a bit, said Ilkay Altintas, the chief data science officer for the San Diego Supercomputer Center, motioning to the book “How to Cook Everything Fast,” which sits prominently on her office desk. Although it might seem like an odd choice of literature for Altintas, she sees it as central to her work. “That’s my dream project,” Altintas said. Link to the full article from UC San Diego Extension.

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Rommie Amaro: The Kavli Foundation Emerging Leader in Chemistry Lecture

Rommie Amaro giving the ACS Kavli Emerging Leader in Chemistry National Lecture at the Spring ACS.

Please see AMBER GPU MD workflow download links

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Rommie Amaro highlighted in Biophysics Week

The Biophysical Society’s Committees for Inclusion and Diversity (CID) and Professional Opportunities for Women (CPOW) have highlighted Rommie Amaro as an outstanding biophysicist who represent the diversity within the field.

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Andrew McCulloch’s article for Biophysics Week

Andrew McCulloch’s article about multiscale modeling for Biophysics Week!

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Ilkay Altintas wins the TCSC Award for Excellence

Ilkay Altintas wins the TCSC Award for Excellence in Scalable Computing for Early Career Researchers

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