Simulation-Based Drug Discovery

National Biomedical Computation Resource (NBCR) and the Theoretical and Computational Biophysics Group (TCBG) are pleased to offer a joint workshop on the theme of Molecular Sulation and Small Molecule Drug Discovery. This week-long intensive program will introduce 12-25 students to principles, methods, and NBCR / TCBG tools for simulating receptors (globular and membrane bound), small molecule docking, rigorous free energy calculations, and drug discovery strategies and workflows. See full article

Data to Structural Models Summer Training Program

NBCR is pleased to offer a Summer Training Program (STP) August 17th to 21st, 2015, on the theme of image-based meshing and structural modeling. This week-long intensive program will introduce 12-20 students to principles, methods, and NBCR tools for generating high-quality three-dimensional meshes for numerical analysis in multi-scale modeling of subcellular, cell, tissue, and organ biophysics. See full article

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 ( and Ludovic Autin (

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

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