Dear Consortium Members and Affiliates,
SBGrid news comes to you today from drizzly, overcast Boston, but no complaints can be made after a string of beautiful fall days filled with crisp air and sunny skies. Before we look ahead to Thanksgiving, please read on for details about the latest software updates, our upcoming REDCAT webinar, a look at Karin Reinisch and her lab at Yale, and a listing of recent publications from SBGrid member labs. Happy Thanksgiving to everyone who has adopted this holiday, and please remember that SBGrid offices will be closed Nov 28-29 to celebrate.
In case you missed part-2 of Frank's Delaglio's webinar on spectral processing and NMRPipe last week, the recorded version has been uploaded to our YouTube channel. We have another NMR webinar in our lineup on December 5th featuring Homay Valafar and a tutorial on Structure Validation of Proteins using REDCAT.
The first citation of SBGrid's eLife article appeared this month, in Titus Boggon's PLOS One publication entitled Substrate and Inhibitor Specificity of the Type II p21-Activated Kinase, PAK6.
Our November SBGrid Tale looks at Karin Reinisch and the work she is doing on membrane trafficking at Yale University School of Medicine. You can read about Karin's work and her long-time association with SBGrid here.
And we have three new members to announce this month: Tom Kirchhausen became our 6th member from Children's Hospital Boston, Yunsun Nam has joined a large contingent from UT Southwestern, and Doug Daniels has put the Broad Institute on our member map. Welcome to our new members!
Software Update
Updates over the last month include the latest versions of CCP4, ARP/wARP, XDS, Spire, FREALIGN and Nessy. We also have updates for Geneious, Coot on Linux, and special nightly builds of Phenix and Rosetta on Linux in order to support the new Phenix-Rosetta refinement tools.
Linux 32-bit and 64-bit and OS X Intel
Chimera has been updated to version 1.8.1 for all platforms. This is mostly a bug fix release that adds support for OS X 10.9. The Chimera release notes have the sordid details.
The XDS data processing tool for X-ray crystallography has been updated to version 20131111. The XDS release notes contain details on the changes.
Spire, the SPIDER Reconstruction Engine from Wadsworth has been updated to version 1.5.5 and should now run properly on 64-bit Linux and OS X Intel machines. There is extensive Spire documentation available.
Nessy, the NMR Relaxation Dispersion Spectroscopy Analysis Software has been updated to version 12.3. It seems that this software is no longer under active development, and the developers are suggesting users switch to NMR relax if they encounter problems. We probably won't update this package in the future.
Linux 64-bit and OS X Intel
The long-awaited CCP4 6.4.0 update is now in place. This update includes new versions of many core tools for structural biology including new versions of REFMAC and Phaser and updates for dozens of related utilities. There was a CCP4 release announcement on the mailing list with some details.
Alongside the CCP4 update, we have updated ARP/wARP to version 7.4.0. Please note that to enable the ARP/wARP interface within CCP4, you'll need to register ARP/wARP.
Geneious has been updated to R7, specifically version 7.0.3. We'll bump it to the 7.0.4 point release in the next few days. The Geneious release notes contain details on the many new features and bug fixes in the R7 release.
Frealign has been updated to version 8.11-130520. This is the latest version for helical processing. The Grigorieff Lab hosts a Frealign web forum for help getting started with the application.
Linux 64-bit
We have installed and configured nightly versions of Phenix and Rosetta to support the newly announced Phenix-Rosetta refinement mentioned in Nature Methods. These experimental versions are not the default, so you'll need to add version overrides in your ~/.sbgrid.conf file:
PHENIX_X=nightly
ROSETTA_X=nightly
You can refresh your memory for setting version overrides on our website. These new features are only available on 64-bit Linux at this time. Phenix generally has very good support for OS X, but Macs seem to be a second tier platform for the Rosetta developers.
Linux 32-bit and 64-bit
Coot has been updated to a recent 0.8-pre nightly release, and a full 0.7.2 release was added at the same time.
Publications
Since our last newsletter, the following publications have appeared from Consortium member labs:
- Ackerson Lab, Coloado State U: Structure-activity relationships for biodistribution, pharmacokinetics, and excretion of atomically precise nanoclusters in a murine model.
- Boggon Lab, YaleU School of Medicine: Substrate and Inhibitor Specificity of the Type II p21-Activated Kinase, PAK6.
- Dreyfuss Lab, UPenn School of Medicine: Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.
- Ealick Lab, Cornell: Structure of a Clostridium botulinum C143S Thiaminase I/Thiamin Complex Reveals Active Site Architecture.
- Frank Lab, ColumbiaU: Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit.
- Gonen Lab, Howard Hughes Medical Institute: Intrinsic disorder within an AKAP-protein kinase A complex guides local substrate phosphorylation.
- Krishnaswamy Lab, UPenn School of Medicine: Modulation of Protein C Activation by Histones, Platelet Factor 4, and Heparinoids: New Insights Into Activated Protein C Formation.
- Kwong Lab, NIH-NIAID: Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus.
- Lacy Lab: VanderbiltU: Clostridium difficile toxin B-induced necrosis is mediated by the host epithelial cell NADPH oxidase complex.
- Lindsley Lab, VanderbiltU: Discovery of the First M5-Selective and CNS Penetrant Negative Allosteric Modulator (NAM) of a Muscarinic Acetylcholine Receptor: (S)-9b-(4-Chlorophenyl)-1-(3,4-difluorobenzoyl)-2,3-dihydro-1H-imidazo[2,1-a]isoindol-5(9bH)-one (ML375).
- Marnett Lab, VanderbiltU: Exploring the molecular determinants of substrate-selective inhibition of cyclooxygenase-2 by lumiracoxib.
- Pascal Lab, Thomas Jefferson U: Targeting PARP-1 allosteric regulation offers therapeutic potential against cancer.
- Sundberg Lab, UMaryland School of Medicine: Recruitment of TLR adapter TRIF to TLR4 signaling complex is mediated by the second helical region of TRIF TIR domain.
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.