Dear Consortium Members and Affiliates,
Yay spring! Nothing more to say on that, but we do have updates for you on several fronts. Read on for the latest on the Quo Vadis Structural Biology? meeting, new HPC/HTC resources, a new SAXS webinar for you to watch, a spotlight on Olve Peersen at Colorado State U, and a software release including several updates and a new application from the 3DNA folks called DSSR.
The Saturday session of Quo Vadis Structural Biology? has now been finalized. We will open with two special presentations from SBGrid Consortium members. Brian Bae from Rockefeller University will talk about the structural basis of the inhibition of E. coli RNA polymerase and Zahra Assur from Columbia University will present on a crystal structure of a novel sulfate transport protein. The Phenix workshop will follow immediately after this short session and we will conclude the meeting around 2PM.
All participants can now register for the poster session using this form. The deadline to submit the title of your poster is May 1st. This session will provide an excellent opportunity to meet other SBGrid consortium members and contributing software developers. Finally, a reminder that a mailing list is available for all out-of-town participants. This mailing list can be used to connect roommates, arrange ride-sharing, and make other travel arrangements. If you are not on the list and would like to be added, please email us at email@example.com. As of today, SBGrid members from 23 institutions have registered to attend the meeting.
To promote awareness about the event and highlight participation of renowned speakers, we would like you to print and post this flyer on your lab bulletin board. Thank you!
Please take a look at the final agenda for the SBGrid/NE-CAT Computing School, which is posted on the SBGrid website along with a list of all currently registered attendees. Registration is still open, so please be sure to reserve your spot soon and tack up this poster to spread the word to others that might be interested.
Since joining the XSEDE Campus Champion program last month, Jason Key has been working to establish cryo-EM workflows at national HPC sites for SBGrid consortium members. Frealign, Relion, and EMAN2/SPARX are currently available. Researchers can prototype their data processing workflow at XSEDE sites and receive a startup allocation before completing the formal application process. If you need HPC or HTC resources for your project, get in touch. Contact Jason at firstname.lastname@example.org.
For those of you that need help getting started using SAXS for structure analysis, we've just uploaded a new webinar to YouTube that offers an introduction to this technique. Tom Grant from the Hauptman-Woodward Medical Research Institute joined us last week to do the recording and he'll connect with us again to record an advanced version soon.
We'll broadcast our next live webinar in a couple of weeks, with Matt Baker from Baylor College of Medicine speaking on Modeling Macromolecular Structures with Gorgon on April 10th.
Also new this month is a story on Olve Peersen. Peersen came late to crystallography, but now uses it as a key tool in his work on viruses at Colorado State University.
Since our last newsletter, we pushed out software updates for HKL2000, 3DNA, CCPNMR, CCP4, ARP/wARP, PHENIX, Schrodinger, Geneious, and EMAN2, and added one new application to the collection: DSSR.
Linux 64-bit and OS X Intel
Schrodinger has been updated to version 2014-1. This version now supports OS X 10.9.
Geneious has been updated to version 7.1.2.
HKL2000 was updated to version 705.
3DNA was upgraded to version 2.1.
CCPNMR has had its internal modules updated to the latest releases.
CCP4 and ARP/wARP were both updated to the latest patch releases.
PHENIX nightly version dev-1645 was added.
EMAN2 nightly version 20140302 was added and made the default version. If enough people kvetch about it, we'll revert the default back to the 2.07 release.
DSSR is a new application defining secondary structures of RNA from three-dimensional coordinates.
The following publications have appeared from Consortium member labs over the past 30 days:
- Bonvin Lab, Utrecht U:
- Integrative Computational Modelling of Protein Interactions.
- HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors.
- Bradner Lab, Dana-Farber Cancer Institute: An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.
- Caflisch Lab, U Zurich: Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk.
- Jia Lab, Queen's U: Protein superglue that holds VWF together.
- Kahne Lab, Harvard U: Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport.
- Lindsley Lab, Vanderbilt U:
- M4 mAChR-Mediated Modulation of Glutamatergic Transmission at Corticostriatal Synapses.
- M5 Receptor Activation Produces Opposing Physiological Outcomes in Dopamine Neurons Depending on the Receptor's Location.
- Identification of Specific Ligand-Receptor Interactions That Govern Binding and Cooperativity of Diverse Modulators to a Common Metabotropic Glutamate Receptor 5 Allosteric Site.
- Luger Lab, Colorado State U: Scm3 deposits a (Cse4-H4)2 tetramer onto DNA through a Cse4-H4 dimer intermediate.
- Markley Lab, U Wisconsin-Madison: Assignments of RNase A by ADAPT-NMR and enhancer.
- Mayer Lab, NICHD NIH: Analysis of Protein Interactions with Picomolar Binding Affinity by Fluorescence-Detected Sedimentation Velocity.
- Phillips Lab, Rice University: Understanding Molecular Recognition of Promiscuity of Thermophilic Methionine Adenosyltransferase, sMAT from Sulfolobus solfataricus.
- Pyle Lab, Yale U: Principles of ion recognition in RNA: insights from the group II intron structures.
- Schwartz Lab, MIT: The stoichiometry of the Nup62 subcomplex of the nuclear pore in solution.
- Sondermann Lab, Cornell U: Ferromagnetic nanoparticles with peroxidase-like activity enhance the cleavage of biological macromolecules for biofilm elimination.
- Walker Lab, Harvard U:
- Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport.
- Microarray Discovery of New OGT Substrates: The Medulloblastoma Oncogene OTX2 Is O-GlcNAcylated.
- Zheng Lab, U Washington: Crystal structure of the plant dual-affinity nitrate transporter NRT1.1.
- Yudin Lab, U Toronto: Site-Specific Integration of Amino Acid Fragments into Cyclic Peptides.
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software.
For the full list of publications please visit the publication section on the SBGrid website.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.