Dear Consortium Members and Affiliates,
We have two announcements for this month: a position available at the Marine Biological Laboratory in Woods Hole, Massachusetts and a free workshop on molecular dynamics held at Stanford University in February.
The updated packages for this month include UCSF Chimera, Coot, PHENIX and SPIDER along with a new graphical interface for SPIDER called Spire. We are also adding some bug fixes for CCP4 and updated probe/reduce utilities for use with the updated Coot.
A senior research scientist position is available at the Marine Biological Laboratory in Woods Hole MA to continue our study on the crystal structures of blood coagulation proteins, particularly Factor VIII (Structure. 2008;16:597-606). This is the protein missing in hemophilia. The candidate should have a sound knowledge and experience in protein X-ray crystallography and protein biochemistry. The work will include preparation of protein-protein complexes, biological assay, crystallization, and structure determination. This laboratory is a satellite of the Center for Hemostasis and Thrombosis located at the Beth Israel DeaconessMedical Center and Harvard Medical School in Boston. A joint appointment at the Marine Biological Laboratory and Harvard Medical School is anticipated.
Funds are available to support this position for up to three years. The successful candidate must have a PhD degree in a relevant field and previous research experience in protein X-ray crystallography. Protein chemistry skills will be important for this position, as will be the importance of working independently.
The position would suit a highly motivated and energetic individual who is keen to work in a multidisciplinary environment involved in structural biology research. Independence and ability to solve experimental problems are critical.
Interested persons should send a detailed CV, covering letter and contact details of three referees to Dr. Bruce Furie at firstname.lastname@example.org.
Want to learn how to quickly set up and run molecular dynamics (MD) simulations? Or are you a veteran to MD who wants to know how to obtain 100X speedups of MD code on graphics processing units (GPUs)?
Whatever your MD background, the free upcoming two-day OpenMM workshop promises to be an exciting, knowledge-filled opportunity, featuring experts from both molecular dynamics and the GPU industry. Day 1, geared for MD developers, presents how MD code can be sped up on GPUs and in particular, with OpenMM freely downloadable, high performance, extensible library that allows MD simulations to run on high performance computer architectures, such as GPUs. Day 2 is for researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the new OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. The workshop will be held on February 12-13, 2009 at Stanford University. Registration is free but spaces are limited. For more details, visit http://simbios.stanford.edu/EventsOfInterest/OpenMMWorkshop.htm.
OpenMM accelerated code running on Nvidia GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., in press.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
UCSF Chimera has been updated to version 1.3.2577. This update includes both X11 and Aqua-based versions for OS X. Links to the documentation, tutorials and releases notes are available on the Chimera home page.
The Probe/Reduce utilities from the Richardson Laboratory have been updated to work with the new Coot to provide atomic packing and clashes functionality.
A few CCP4 fixes have been applied to the updated CCP4 6.1.0 which became available last month. These include bug fixes for sfcheck and the addition of the BALBES database for molecular replacement.