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. But new work by a research team at the National Biomedical Computation Resource (NBCR) at UC San Diego has taken a big step in this Grail’s direction. In basic terms, they are studying the biochemistry of how proteins move, how that movement relates to their conformational shapes (which determine their functions), and how an allosteric ligand can influence those movements. See full article

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

Older posts «