Dear Consortium Members and Affiliates,
As we say goodbye to July and note that summer is halfway past we have a few notes of interest to pass along. We have news on changes to the operating systems we support, several new videos posted to YouTube along with information on our webinar schedule for the fall, a story on James Chen at OHSU, 4 new members to welcome, and a software release that includes several updates and one new application.
We are also presenting SBGrid posters tomorrow at the 20th Annual Harvard Structural Biology Retreat. If you are attending the event please stop by!
Our technical team is hard at work preparing for the release of several new operating systems, including Mac OS X 10.10 (Yosemite) and, for our Linux users, Red Hat 7, CentOS 7, and Scientific Linux (SL) 7. If your group is currently using Mac OS 10.6 or earlier, or version 5.x of any of the Linux flavors, we recommend that you plan an upgrade soon.
-
Mac: the public beta of Yosemite is now available and the official release is slated for the fall. SBGrid currently supports versions 10.6-10.9 and plan to add Yosemite by year end. Once Yosemite support is complete we will slowly phase out support for Mac OS 10.6 and concentrate our efforts on supporting the most recent 64-bit versions of the Mac OS.
-
Linux: we are currently supporting the two most recent versions of Red Hat/CentOS/SL (versions 5 & 6) and will add support for version 7 later this year with a plan to stop supporting version 5 after allowing several months to transition.
More details on how SBGrid will handle these new operating systems can be found here, including information about applications that require specific 32-bit kernel extensions. If you are interested in upgrading to Red Hat/CentOS/SL version 7, for which testing is currently underway, or Yosemite, please contact us at bugs@sbgrid.org. You can also find a current list of SBGrid-supported operating systems at: https://www.sbgrid.org/wiki/software/operatingsystems
We've published several new recordings on our YouTube channel this month, adding three more recordings from our June Computing School. We hope to have all the remaining lectures from the event posted by the end of August. Also new on the SBGridTV channel is a copy of the webinar that was broadcast on July 17th featuring Kazutaka Katoh and Daron Standley from Osaka University on MAFFT/MAFFTash structure-informed multiple sequence alignment.
Last Friday, in collaboration with the folks across the river at Harvard University, we also recorded a talk by Dr. Robin Owen from Diamond Light Source entitled “Hot beams and cool crystals. Faster and smaller macromolecular crystallography at Diamond Light Source". Thanks to Goran Malojcic for organizing this event and allowing us to share it with SBGrid members.
Webinars are on hold for the month of August, but we'll kick off the new season in September with two talks from Geneious R7 Application Scientist Christian Olsen. He'll cover Sequence Analysis on September 9th and return for a session on Molecular Cloning on September 23rd. Additional details on these webinars will be posted on the SBGrid website.
For our July tale we talked with James Chen in his new lab at the Oregon Health and Science University where he's pushing the boundaries of EM data analysis both technically, to increase the speed of data collection, and methodologically, to achieve super-resolution in EM. Chen's software application PARTICLE is included in the SBGrid suite.
We've had four new members join since our last newsletter. Barry Honig became our fifth member at Columbia, Phoebe Chen and David Wilson have joined the ranks from La Trobe, and Cornell has grown to seven members with the addition of Josh Chappie. Welcome to our new members!
Our software update this month included new releases from CCP4, CCP4MG, DSSR, and RELION. You'll also find one new application: the Integrative Genomics Viewer. More details below.
Software Changes
CCP4 6.4.0 patch 19 corrects convergence issues in ctruncate and includes a new rebuild option using SHELXE for phase improvement and c-alpha trace.
CCP4MG was updated to version 2.9.0 and includes a bevy of user interface improvements along with significant improvements to ProSMART, including new tool buttons and graphs to visualize results. Complete details can be found in their release notes.
DSSR is now at version 1.1.3-2014, which is the version that Xiang-Jun Lu demonstrated during his June webinar. You can find the webinar posted on our YouTube channel
Integrative Genomics Viewer (IGV version 2.3.34), which comes from the Broad Institute, was recently added to the SBGrid collection. This software can be used for interactive exploration of large, integrated genomic datasets from data of various types, including array-based and next-generation sequence data, and genomic annotations. Please take a look at the IGV website for more information on this program.
RELION was updated to version 1.3. No news on the changes included in this release but they do warn of a known bug in the autopicking program.
Publications
The following publications have appeared from Consortium member laboratories over the past 30 days:
- Alexandre Bonvin's Group, Utrecht U: Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface.
- James Bradner's Group, Dana-Farber Cencer Institute:
- BET protein antagonist JQ1 is synergistically lethal with FLT3 tyrosine kinase inhibitor (TKI) and overcomes resistance to FLT3-TKI in AML cells expressing FLT-ITD.
- Epigenetic targeting of Hedgehog pathway transcriptional output through BET bromodomain inhibition.
- Inhibition of bromodomain proteins for the treatment of human diffuse large B-cell lymphoma.
- Amedeo Caflisch's Group, U Zurich: Spontaneous Self-Assembly of Engineered Armadillo Repeat Protein Fragments into a Folded Structure.
- Walter Chazin's Group, Vanderbilt U: Acinetobacter baumannii Response to Host-Mediated Zinc Limitation Requires the Transcriptional Regulator Zur.
- Catherine Drennan's Group, MIT: Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity.
- Oliver Ernst's Group, U Toronto: Coupling of G Proteins to Reconstituted Monomers and Tetramers of the M2 Muscarinic Receptor.
- Stephen Harrison's Group, Harvard Medical School: Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains.
- Tina Iverson's Group, Vanderbilt U: A conserved phenylalanine as relay between the α5 helix and the GDP binding region of heterotrimeric Gi protein α subunit.
- Daniel Kahne's Group, Harvard U: Bacterial cell wall. MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis.
- John Kuriyan's Group, UC Berkeley: Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics.
- Peter Kwong's Group, NIH: Binding mode characterization of NBD series CD4-mimetic HIV-1 entry inhibitors by X-ray structure and resistance study.
- David Lambright's Group, UMass Medical School, Drosophila Sirt2/mammalian SIRT3 deacetylates ATP synthase β and regulates complex V activity.
- Lawrence Marnett's Group, Vanderbilt U: Structure and Stereochemical Determination of Hypogeamicins from a Cave-Derived Actinomycete.
- Par Nordlund, Nanyang Technological U: Structural and Biochemical Characterization of Human PR70 in Isolation and in Complex with the Scaffolding Subunit of Protein Phosphatase 2A.
- Andreas Plüeckthun's Group, U Zurich: Spontaneous Self-Assembly of Engineered Armadillo Repeat Protein Fragments into a Folded Structure.
- Michael Rosen's Group, UT Southwestern Medical: Retromer Binding to FAM21 and the WASH Complex Is Perturbed by the Parkinson Disease-Linked VPS35(D620N) Mutation.
- Frank Sicheri's Group, U Toronto: Structural basis for the recruitment of glycogen synthase by glycogenin.
- Brian Smith's Group, La Trobe U: Inhibition of Plasmepsin V Activity Demonstrates Its Essential Role in Protein Export, PfEMP1 Display, and Survival of Malaria Parasites.
- Lawrence Stern's Group, UMass Medical School: Susceptibility to HLA-DM is determined by a dynamic conformation of major histocompatibility complex class II molecule bound with peptide.
- Oleg Tsodikov's Group, U Kentucky: 2',6'-Dihalostyrylanilines, Pyridines, and Pyrimidines for the Inhibition of the Catalytic Subunit of Methionine S-Adenosyltransferase-2.
- Gerhard Wagner's Group, Harvard Medical School:
- Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G.
- The LxVP and PxIxIT NFAT Motifs Bind Jointly to Overlapping Epitopes on Calcineurin's Catalytic Domain Distant to the Regulatory Domain.
- Hao Wu's Group, Children's Hospital Boston: MTDH-SND1 Interaction Is Crucial for Expansion and Activity of Tumor-Initiating Cells in Diverse Oncogene- and Carcinogen-Induced Mammary Tumors.
- Hongtao Yu's Group, UT Southwestern Medical School: Genome-wide siRNA screen reveals coupling between mitotic apoptosis and adaptation.
- Andrei Yudin's Group, U Toronto: Small Heterocycles in Multicomponent Reactions.
- Ming Zhou's Group, Baylor College of Medicine: Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1.
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.