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. CellPACK, published recently in Nature Methods, enables researchers to construct mesoscale systems with new levels of detail and realism, addressing a major challenge for researchers who are interested to integrate data across diverse scales of biological organization. A full press release can be found here.

CellPACK is a biological packing algorithm optimized to pack molecular structures and other data types into biological volumes. CellPACK creates 3D models of the cellular mesoscale. In this image cellPACK generates an editable model of HIV by packing from a recipe of molecular ingredients1 into the ultrastructure of an HIV envelope surface. Image created by Graham Johnson (grahamj.com) and Ludovic Autin (mgl.scripps.edu).

Amber Workshop

NBCR and NVIDIA are proud to co-sponsor a Hands-on AMBER molecular dynamics workshop Dec 15-18, 2014 at UCSD. Come learn both basic techniques, such as how to run molecular dynamics with AMBER's NVIDIA GPU code and how to use VMD to visualize AMBER trajectories, as well as more advanced topics, such as how to use BioKepler workflows for your MD runs and explore advanced sampling techniques such as Accelerated Molecular Dynamics (aMD). See workshop website

How 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. See full article

Experimentation Meets Computation

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.

Each pumping cycle is initiated when calcium is released from storage sites in the muscle cells and binds to the protein troponin of the contractile filaments. Troponin is the protein complex that acts as a switch from relaxation to contraction in heart muscle and is the central regulator of the magnitude of contraction. See full article

Focus on Scientific Workflows

Ilkay Altintas’ work as Director of SDSC’s Scientific Workflow Automation Technologies Laboratory that has earned her particular acclaim. A scientific workflow is software composed of a series of computational and/or data manipulation tools or steps to produce an application that can be run especially on high-performance computers to produce data for subsequent analysis or comparison with other data sets. See full article

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