Dear Consortium Members and Affiliates,
Our May update is a short one with some final notes for those planning to attend next week's Computing School, some webinar news, and a software update for you.
We are eager to welcome many of you to the SBGrid/NE-CAT Computing School next week. Please take a peek at the final program, which includes a map of the area, speaker abstracts, a list of poster presenters, and other useful info. We also have advance meeting materials from a couple of our speakers (Phil Evans and Jim Pflugrath), which can be accessed here. Please contact us at email@example.com with any questions. See you on Thursday the 5th!
Last week Nat Echols gave a webinar presentation on refining challenging structures with Phenix and Rosetta. If you missed the live presentation, you can now watch the recorded version on YouTube. Our June webinar is scheduled for the 26th and will feature Xiang-Jun Lu on DSSR, a new program that extends the functionality of 3DNA.
We pushed out a software update a couple of weeks ago that included updates to CCP4, Chimera, Xmipp, MGLTools, EM-BFACTOR, Graphviz, Spider, and Phenix as well as two new applications: Knusp and RASPnmr.
This month we are welcoming two new members. Gabby Rudenko has re-joined the Consortium, now from her new lab at University of Texas Medical Branch at Galveston and Jue Chen joins us as she makes her transition from Purdue to Rockefeller University. Welcome to our new members!
Knuspr, one of Tim Gruene's recent projects, was added to the collection. Knuspr can be used in combination with RCrane to "help you find the positions of phosphates and bases in electron density maps."
RASPnmr was also added to the default SBGrid install. RASPnmr is a tool for protein NMR spectroscopy that uses "structure-based chemical shift predictions to solve the backbone resonance assignment problem."
CCP4 6.4.0 has been updated to include patch 15.
Chimera was updated to version 1.9 In this version users will be able to more easily enable multiple NVIDIA graphics cards and the application will now support Intel's Ivy Bridge CPUs and GraphicsEnabler detection for NVIDIA's new GeForce GTX 680.
Xmipp is now at version 3.1
MGLTools was updated to version 1.5.7rc1
EM-BFACTOR version 2014_05_05 includes a 64-bit build for OSX, which allows the user to sharpen large maps.
In Graphviz version 2.36.0 the process of packing connected components in the dot program is now more consistent with other layout tools.
Spider version 11.0 includes a bevy of new documentation with sample operations, inputs, and outputs along with some new file conversion options.
Phenix nightly build 1.9-1692 includes better documentation, improved AutoSol performance, Rosetta refinement, similarity restraints, and automatic ligand linking. You'll also find two new tools: a new composite omit map tool and command line MolProbity.
The following publications have appeared from Consortium member laboratories over the past 30 days:
- Demetrios Braddock's Group: Metformin suppresses gluconeogenesis by inhibiting mitochondrial glycerophosphate dehydrogenase.
- Samuel Butcher's Group, U Wisconsin-Madison: Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution.
- Walter Chazin's Group, Vanderbilt U: Structural Analysis of Replication Protein A Recruitment of the DNA Damage Response Protein SMARCAL1.
- Jennifer Doudna's Group, U California, Berkeley:
- Insights into RNA structure and function from genome-wide studies.
- Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.
- CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.
- Steve Ealick's Group, Cornell U: Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.
- Brant Eichman's Group, Vanderbilt U: A structure-specific nucleic acid-binding domain conserved among DNA repair proteins.
- Qing Fan's Group, Columbia U: Heterodimeric coiled-coil interactions of human GABAB receptor.
- Steve Harrison's Group, Harvard Medical School: Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic.
- Tom Kirchhausen's Group, Children's Hospital Boston: Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic.
- Marc Kvansakul's Group, La Trobe U: Structural Insight Into BH3-Domain Binding of Vaccinia Virus Anti-Apoptotic F1L.
- Craig Lindsley's Group, Vanderbilt U: A Novel Class of Succinimide-Derived Negative Allosteric Modulators of Metabotropic Glutamate Receptor Subtype 1 Provides Insight into a Disconnect in Activity between the Rat and Human Receptors.
- Wayne Marasco's Group, Dana-Farber Cancer Institute:
- Molecular Signatures of Hemagglutinin Stem-Directed Heterosubtypic Human Neutralizing Antibodies against Influenza A Viruses.
- Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution.
- Jarrod Smith's Group, Vanderbilt U: Automated Structure Refinement for a Protein Heterodimer Complex Using Limited EPR Spectroscopic Data and a Rigid-Body Docking Algorithm: A Three-Dimensional Model for an Ankyrin-CDB3 Complex.
- Steven Smith's Group, Queen's U: Structure of the Small Dictyostelium discoideum Myosin Light Chain MlcB Provides Insights into MyoB IQ motif Recognition.
- Michael Stone's Group, Vanderbilt U: Structures of Exocyclic R,R- and S,S-N(6),N(6)-(2,3-Dihydroxybutan-1,4-diyl)-2'-Deoxyadenosine Adducts Induced by 1,2,3,4-Diepoxybutane.
- Gerhard Wagner's Group, Harvard Medical School: Constitutively oxidized CxxC motifs within the CD3 heterodimeric ectodomains of the T cell receptor complex enforce the conformation of juxtaposed segments.
- Andrew H-J Wang's Group, Academia Sinica:
- Squalene Synthase As a Target for Chagas Disease Therapeutics.
- Proposed Carrier Lipid-Binding Site of Undecaprenyl Pyrophosphate Phosphatase from Escherichia coli.
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.