Dear Consortium Members and Affiliates,
As we announced last week, the first complete description of our Consortium was just published in eLIFE. Please cite this paper in all work that has benefited from SBGrid-supported software and share it with your colleagues who might want to join the consortium as well. It has been another productive month for SBGrid laboratories. We had 18 papers published in various journals. A special highlight goes to Mike Eck and his paper in PNAS describing the receptor tyrosine kinase (RTK) "superacceptor" activity (see the list of all SBGrid publications below).
Geneious, commercial bioinformatics software suite, is coming soon to SBGrid! Ten floating tokens will be available to all non-commercial laboratories starting in October and it will be possible to purchase access to additional tokens with an SBGrid discount. A webinar from the developers at Geneious is also being planned for October. More details will follow soon.
In this month's SBGrid Tale we hear from Assistant Professor Mishtu Dey at the University of Iowa, where she set up her new lab about 2 years ago. You can read her story here.
We had our first successful webinar using the new FUZEBOX webinar hosting software for Andrea Thorn's presentation on SHELX-2013. If you attended the meeting, we would love to hear your feedback. If you missed the presentation, the recording has been added to our YouTube channel.
In other webinar news, we have a 2-part webinar scheduled for November 7th and 14th that will feature Frank Delaglio and NMRPipe. See the SBGrid website for complete details. Apologies for the failed attempt with Paul Emsley. We tried our usual WebEx program and the new Fuze application and neither would play nice with Paul's computer. We hope to soon reschedule or publish a recorded version of his Coot presentation.
Registration Required! We will be removing all EMBL-funded applications from our default software installation at the request of their licensing department. If you use ARP/wARP, HKL2MAP, ATSAS, BEST, or ESCET, we can continue to install and support these applications for you, but you will first need to register on their websites. See complete details here: http://www.sbgrid.org/news/article/id=382
Anthony Rappe from Colorado State is the newest member to join SBGrid, while James Hurley has continued his membership in his move from NIH to UC Berkeley. Welcome to our new members!
Our August 27th software update included new versions of NUCPLOT, DSSP, SIMPLE, PDB2PQR, CCPNMR, PHYLIP, relax, adxv, FASTA, MammothMult, PHENIX, and MAFFT
Notable Software Changes
Single-particle IMage Processing Linux Engine (SIMPLE), developed at Stanford, complements other developments in EM reconstruction. In this new version (http://simple.stanford.edu/) the common lines-based routines were replaced with a new ab initio reconstruction method called PRIME (PRobabilistic Initial 3D Model Generation for Single-Particle Cryo-Em). You can read more about PRIME in a recent article in Structure.
We have installed another fairly major update to Phenix (dev-1448). This is the second pre-release installation of the major release 1.8.3. Changes in comparison to 1224 pre-release include an omit_selection keyword in phenix.refine and optional harmonic restraints for simulated annealing omit map calculations. AutoSol and AutoBuild now allows one to specify a different number of copies of different chains while AutoSol and Phaser have incorporated speed enhancements. The Restraints Editor Especially Ligands (REEL) is easier to use and supports cis/trans E/Z enantiomers and MR-Rosetta will speed up with an optional flag to ignore long-running sub-processes. In addition the PDBTools utilities remove_alt_confs and truncate_to_poly_ala are now compatible with other model modifications. The official 1.8.3 release of Phenix will be announced by SBGrid in October.
Major Update: The NMR application relax is used to study molecular dynamics of proteins and nucleic acids. This application was updated to version 3.0.0, which marks the first release of the new relax 3 series. While the majority of the code has been reorganized the user interface remains relatively unchanged. Please visit the developer's website for the complete list of changes.
DSSP is an application used to assign secondary structure that was originally developed by Wolfgang Kabsch and Chris Sander. DSSP underwent a major rewrite in 2011. We updated to version 2.0.4 back in March, and the newest version 2.2.0 incorporates additional fixes.
NUCPLOT generates schematics of protein-nucleic acid interactions and was developed by Roman Laskowski and Nicholas Luscombe. NUCPLOT was updated to version 1.1.4. For a list of other applications developed by Roman Laskowski, including Ligprep for protein-ligand interactions, please visit his website at the European Bioinformatics Institute at Cambridge, UK.
We have installed the current version of PDB2PQR, an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Support for PROPKA 3.0 pKa software and several improvements to the command line extensions functionality were introduced. Please visit the developer's website for usage instructions.
Since our last newsletter, the following publications have appeared from Consortium member labs:
- Blaha Lab, UC Riverside: The E3 Ubiquitin Ligase XIAP Restricts Anaplasma phagocytophilum Colonization of Ixodes scapularis Ticks.
- Darst Lab, Rockefeller U: Crystallographic analysis of an RNA polymerase σ-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes.
- Eck Lab, Dana-Farber Cancer Institute: Mechanism for activation of mutated epidermal growth factor receptors in lung cancer.
- Holden Lab, UWisconsin-Madison: pH-rate profiles support a general base mechanism for galactokinase (Lactococcus lactis).
- Howell Lab, UToronto: Functional Characterization of Staphylococcus epidermidis IcaB, a De-N-acetylase Important for Biofilm Formation.
- Krishnaswamy Lab, UPenn School of Medicine: Membrane Binding by Prothrombin Mediates its Constrained Presentation to Prothrombinase For Cleavage.
- Kwong Lab, NIH: Elicitation of HIV-1-neutralizing antibodies against the CD4-binding site.
- Kwong Lab, NIH: Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning.
- Lemmon Lab, UPenn School of Medicine: Mechanism for activation of mutated epidermal growth factor receptors in lung cancer.
- Lindsley Lab, Vanderbilt U:
- Discovery of 'molecular switches' within a GIRK activator scaffold that afford selective GIRK inhibitors.
- Heterotropic Activation of the Midazolam Hydroxylase Activity of CYP3A by a Positive Allosteric Modulator of mGlu5: In Vitro to In Vivo Translation and Potential Impact on Clinically Relevant Drug-Drug Interactions.
- Lu Lab, UPenn School of Medicine: Tuning voltage-gated channel activity and cellular excitability with a sphingomyelinase.
- Nikolov Lab, Memorial Sloan-Kettering Cancer Institute: Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5.
- Nordlund Lab, Nanyang Technological University: Structural insights into substrate recognition in proton-dependent oligopeptide transporters.
- Rees Lab, CalTech: The Sixteenth Iron in the Nitrogenase MoFe Protein.
- Shamoo Lab, Rice U: Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance.
- Sliz Lab, Harvard Medical School: Collaboration gets the most out of software.
- Walensky Lab, Dana-Farber Cancer Institute: Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer.
- Yudin Lab, UToronto: Stereocontrolled Synthesis of 1,2- and 1,3-Diamine Building Blocks from Aziridine Aldehyde Dimers.
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.