Dear Consortium Members and Affiliates,
We're taking a break from our webinar series this month, but will resume in September with a Coot presentation from Paul Emsley on September 12th followed by Andrea Thorn's webinar on September 19th describing the new features in SHELX-2013. The fall line-up is still in the works, so please be sure to chime in if you would like to learn about a particular software program in the SBGrid collection
We've just added a new Publications section to the newsletter to highlight the work being done in Consortium laboratories, with a listing of 19 new papers produced in the last couple of months. Please be sure to check it out.
We have a new pilot project in the works with an aim to offer Geneious molecular cloning software to SBGrid members. Details are still being finalized, but we hope to kick things off with a Geneious webinar in October followed by an option to install software on a trial basis. Software will be available via floating tokens and we will monitor usage during this trial to determine what our budget can support and how users can buy in to the program.
The August SBGrid Tale profiles Brian Crane, Professor at Cornell University. Brian describes his interest in circadian clocks and chemotaxis systems and his wonder at discovering how the smallest changes in their protein networks prompt alterations in behavior.
Our new YouTube channel has now been populated with all of the recordings from our software webinar series. We will expand this resource in the coming months, adding SBGrid tutorials, linking to previously recorded presentations by developers, and recording new webinars. Please take a look and subscribe to the channel to be notified when new videos are added.
Three new consortium members joined during the past month. Nina Leksa became our 5th member at Biogen and Anthony Rappe our 6th at Colorado State University. Sirano Dhe-Paganon also joined as the head of Dana Farber's new Structural Biology Core. Welcome to our new members!
We pushed out a big software update on July 24th, which included updates to CCPNMR, Relion, EMAN2, xdsme, PHENIX, XIA2, CTF tools, Auto3DEM, Delphi, MODELLER, Probe, and Reduce. We also added four new software applications to the collection: XDSGUI, FASTModelFree, TkDiff, and VMD-Xplor.
Notable Software Changes
We have installed a new graphical user interface for the XDS data processing package. This new interface, called XDSGUI, can be started from a command prompt and will allow you to submit XDS jobs and review output files. Another data processing wrapper, XIA2, has been updated to version 0.3.6.1 and includes improved compatibility with XDS. Phenix was updated to version 1426. This new version supports improved bulk solvent mask calculations, which can further improve your structure statistics. The graphics user interface has also been improved to include pause and resume buttons and functionality to convert to and from mmCIF files. In phenix.refine, new local and global real-space refinement methods were added.
RELION, a program used to refine 3D reconstructions and 2D class averages, which was developed by the Scheres laboratory at MRC, was updated to version 1.2. No changelog was provided, but you can visit the developer's website for tutorials and documentation. Auto3DEM, an automated image reconstruction system developed by Dr. Tim Baker's group at UCSD, was updated to version 4.03. This new release extends limits on the number of micrographs and parameter files. Other updates include changes in the autopp procedure adding a new dilation parameter for the autobox routine that can automatically delete temporary files, and a revised auto3dem procedure that splits reconstruction and alignment into two separate steps and introduces several dynamic parameters. Fixes were also applied to other procedures in the package. Version 2.07 of EMAN2 includes an improved e2refine_evenodd test routine that should be used for all structures. Other improvements include better DM3 and DM4 support, keyboard shortcuts in the e2ctf.py GUI, and a 'probe' mode in 2D image display.
FASTModelfree, a program to assist in the analysis of spin relaxation data that was developed by Patrick Loria at Yale, was updated to version 1.2. VMD-Xplor was upgraded to version 1.72. According to the author's website at NIH, "this package allows manual manipulation of the protein structures to satisfy experimental NMR data, and can also be used to visualize the goodness of fit of a particular model to given restraints." The new release adds the ability to SVD fit and visualize dipolar coupling restraints and also includes several functionality improvements in VMD. CCPNMR was updated to version 2.3.0.
Delphi, an application for modeling electrostatic potential that was developed by Emil Alexov at Clemson University, was upgraded to version 6.0. Several new features, including multi-dielectric code, geometric-shaped charge distributions, and non-linear PBE solving routine, were introduced. Modeller, a program for comparative protein structure modeling developed by the Sali group at UCSF, was upgraded to version 9.12. This release is primarily a bugfix and is only supported on Linux and OS X 10.6 or later. We also added a new application, TkDiff, a graphical end program to the diff file comparison utility. Probe and Reduce, two applications developed by Jane and David Richardson that are used to evaluate atomic packing and for adding hydrogens, were upgraded to the most recent release.
Since our last newsletter, Consortium member labs have produced the following publications:
- Ban Lab, ETH Zurich: The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A.
- Bingman Lab, UWisconsin-Madison: Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation.
- Chang Lab, Academia Sinica: Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors.
- Darst Lab, Rockefeller U: Structure and function of CarD, an essential mycobacterial transcription factor.
- Doudna Lab, UC Berkeley: High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.
- Krishnaswamy Lab, UPenn School of Medicine: Membrane Binding by Prothrombin Mediates its Constrained Presentation to Prothrombinase For Cleavage.
- Kwong Lab, NIH:
- Heavy chain-only IgG2b-llama antibody effects near-pan HIV-1 neutralization by recognizing a CD4-induced epitope that includes elements of both CD4- and co-receptor-binding sites.
- Residue-Level Prediction of HIV-1 Antibody Epitopes Based on Neutralization of Diverse Viral Strains.
- Lambright Lab, UMass Medical School: Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors.
- Lemmon Lab, UPenn School of Medicine: Receptor tyrosine kinases with intracellular pseudokinase domains.
- Marnett Lab, Vanderbilt U: Substrate-selective COX-2 inhibition decreases anxiety via endocannabinoid activation.
- Medalia Lab, UZurich:
- Experimental analysis of co-evolution within protein complexes: The yeast exosome as a model.
- The role of integrin-linked kinase in the molecular architecture of focal adhesions.
- Patel Lab, Memorial Sloan Kettering Cancer Center: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids.
- Sattler Lab, Helmholtz Zentrum Muenchen: Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity-Optimized NMR Pulse Sequences.
- Schwartz Lab, MIT: Optimized E. coli expression strain LOBSTR eliminates common contaminants from His-tag purification.
- Southworth Lab, UMichigan: The E3 Ubiquitin Ligase CHIP and the Molecular Chaperone Hsc70 Form a Dynamic, Tethered Complex.
- Wang Lab, Dana Farber Cancer Institute: The sequence signature of an Ig-fold.
- Wucherpfennig Lab, Dana Farber Cancer Institute: Cracking the code of human T-cell immunity.
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.