Dear Consortium Members and Affiliates,
As April comes to a close we have news on several fronts to pass along. We have a new Schrodinger workshop and deadlines that are fast approaching for our June Computing School, a webinar newly posted and another scheduled for May 13th, a story featuring Catherine Drennan, Professor at MIT, a software release with 9 updates, SBGrid citations from the Zimmer and Kvansakul groups, and two new SBGrid member labs.
Last call for the SBGrid/NE-CAT Computing School! You can now choose between the Phenix or Schrodinger workshops for our Saturday session. The Schrodinger workshop was just added to the agenda. It will be limited to 20 attendees and will focus on Improved Structural Modeling Using BioLuminate. We'll be adding BioLuminate to the SBGrid installation in July on a trial basis, and hope this workshop will allow members to begin to use the software immediately.
We're in the final stages of planning for the computing school and have several deadlines and bits of information for you to keep in mind:
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May 4th - Lodging deadline:
- The block of rooms that we have reserved at the Inn at Longwood will be released on May 4th, after which the rates will increase and it may become difficult to find a room near the meeting site. RESERVE LODGING HERE.
- If you are looking for a roommate or hoping to plan a ride-share, you can connect with other meeting participants by posting to our google group at qv14-travel@hkl.hms.harvard.edu.
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May 7th - Registration deadline: last day to register for the Computing School, Poster Session, and Phenix/Schrodinger Workshops.
- Register for the SBGrid/NE-CAT Computing School
- Register for the Poster Session
- Register for the Saturday workshop (Phenix or Schrodinge/BioLuminate): The Saturday workshops are free for participants attending the Thursday/Friday sessions, but you must register to attend by sending an email to events@sbgrid.org. If you are uncertain about your status, the list of registered attendees on our website has been updated to indicate participation in special sessions.
In webinar news, we recently uploaded Matt Baker's April presentation on the molecular modeling software Gorgon to our YouTube channel. Please connect and watch at your leisure. And be sure to connect with us on May 13th at 12 noon EST to hear Nat Echols's presentation on Refinement of challenging structures with Rosetta and Phenix. For those of you on the Harvard campus, join us for lunch in LHRRB208, where we'll be streaming the presentation on the big screen and fielding questions for the speaker Q&A at the end of the webinar.
For our April SBGrid Tale we get a look into the surprising background of MIT professor Catherine Drennan, who got her start as an Iowa high school teacher responsible for all things concerning science, the most memorable of which included birthing hogs!
We recently released a small software update for the following applications: HKL2000, R, SITUS, Geneious, EPMR, SSAHA2, Autodock, PHENIX. The application BUSTER has also been added to the collection, on an individually licensed basis. More details about these software updates are included below.
SBGrid received two new citations this month, one from Marc Kvansakul's group at La Trobe University, in his paper describing tumor cell lysis induced by plant defensin eLife. 2014; 3: e01808, the other appeared in Jochen Zimmer's paper out of University of Virginia School of Medicine, which offers insight into how the bacterial signaling molecule cyclic di-GMP activates cellulose synthase NSMB 2014. Many thanks for supporting our efforts to develop new tools for structural biologists by remembering to cite SBGrid's eLife paper.
And, finally, we've had two new members join in the past couple of weeks, each representing an institution new to SBGrid: David Jeruzalmi from City College of New York and James Fraser at University of California, San Francisco. Welcome to our new members!
Software Changes
Linux 64-bit and OS X Intel
PHENIX has been updated to version 1.9-1678. This is very close to the final 1.9 release version, but the release was not finalized as of this update. We'll install the full release version when it becomes available.
HKL2000 has been updated to version 2000.0.98.705a. This version supports the latest detectors at SERCAT, but it requires a new license from HKL Software to enable those detectors. You can use the access_prod tool in the HKL installation to generate a license request.
BUSTER version 1.10.1 has been added to the software tree on an individually licensed basis. BUSTER is freely available to academic labs, but each lab must register with Global Phasing. To enable this software in your installation, please submit a license request to http://www.globalphasing.com/autoproc/licence/request.html, then copy your license file to /programs/local/buster/buster_licence, and the software will start working.
iMosflm has been updated to version 7.1.1. This release includes fixes to the QuickSymm and QuickScale options and eliminates a pesky pop-up bug.
R has been updated to version 3.0.3 and includes a number of new features and bug fixes, which are nicely detailed here
SITUS is now at version 2.7.2.
Geneious had a minor update to version 7.1.4. The changelog details several bug fixes and improvements in stability.
EPMR has been updated to the latest version 13.07.
SSAHA2 also received a minor update to version 2.5.5.
Autodock has been bumped to version 4.2.5.1. This release fixes a bug in the intermolecular desolvation energy term calculation with a caution that users should re-do any calculations that were done using 4.2.5.
Publications
The following publications have appeared from Consortium member laboratories over the past 30 days:
- Ackerson Laboratory, Colorado State U: Size-Focusing Synthesis of Gold Nanoclusters with p-Mercaptobenzoic Acid.
- Adams Laboratory, U Chicago: Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4.
- Anderson Laboratory, Yale U School of Medicine: Fluorescence resonance energy transfer studies of DNA polymerase beta: The critical role of fingers domain movements and a novel non-covalent step during nucleotide selection.
- Arndt Laboratory, Biogen, Idec: Structure of the LINGO-1-anti-LINGO-1 Li81 antibody complex provides insights into the biology of LINGO-1 and the mechanism of action of the antibody therapy.
- Bonvin Laboratory, Utrecht U: Information-driven modeling of large macromolecular assemblies using NMR data.
- Bradner Laboratory, Dana-Farber Cancer Institute: Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation.
- Darst Laboratory, Rockefeller U:Promoter melting by an alternative σ, one base at a time.
- Egli Laboratory, Vanderbilt U: Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase η.
- Eichman Laboratory, Vanderbilt U: 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3.
- Forman-Kay Laboratory, U Toronto: The Effect of Intrachain Electrostatic Repulsion on Conformational Disorder and Dynamics of the Sic1 Protein.
- Fox Laboratory, U Wisconsin-Madison: Biochemical Properties and Atomic Resolution Structure of a Proteolytically Processed β-Mannanase from Cellulolytic Streptomyces sp. SirexAA-E.
- Gonen Laboratory, Howard Hughes Medical Institute: Amphotericin forms an extramembranous and fungicidal sterol sponge.
- Hogle Laboratory, Harvard Medical School: An Interaction between Glutathione and the Capsid Is Required for the Morphogenesis of C-Cluster Enteroviruses.
- Jia Laboratory, Queen's U:Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates.
- Kornberg Laboratory, Stanford U: Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic Laboratory independent mechanisms.
- Kvansakul Laboratory, La Trobe U: Phosphoinositide-mediated oligomerization of a defensin induces cell lysis.
- Lindsley Laboratory, Vanderbilt U: Discovery, Synthesis and Characterization of a Highly Muscarinic Acetylcholine Receptor (mAChR)-Selective M5 -Orthosteric Antagonist, VU0488130 (ML381): A Novel Molecular Probe.
- Marnett Laboratory, Vanderbilt U: GRASr2 Evaluation of Aliphatic Acyclic and Alicyclic Terpenoid Tertiary Alcohols and Structurally Related Substances Used as Flavoring Ingredients.
- Moazed Laboratory, Harvard Medical School: Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.
- Piccirilli Laboratory, U Chicago:
- Evidence for a group II intron-like catalytic triplex in the spliceosome.
- Synthesis and Incorporation of the Phosphoramidite Derivative of 2'-O-Photocaged 3'-S-Thioguanosine into Oligoribonucleotides: Substrate for Probing the Mechanism of RNA Catalysis.
- Quan Group, Biogen Idec: Structure of the LINGO-1-anti-LINGO-1 Li81 antibody complex provides insights into the biology of LINGO-1 and the mechanism of action of the antibody therapy.
- Schlessinger Laboratory, Yale U School of Medicine: The docking protein FRS2α is a critical regulator of VEGF receptors signaling.
- Sodroski Laboratory, Dana-Farber Cancer Institute: CD4-mimetic Small Molecules Sensitize Human Immunodeficiency Virus (HIV-1) to Vaccine-elicited Antibodies.
- Southworth Laboratory, U Michigan: Architecture of the Nitric Oxide Synthase Holoenzyme Reveals Large Conformational Changes and a Calmodulin-Driven Release of the FMN Domain.
- Springer Laboratory, Children's Hospital, Boston: Application of encoded library technology (ELT) to a protein-protein interaction target: Discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists.
- Sundberg Laboratory, U Maryland School of Medicine: Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies.
- Tsodikov Laboratory, U Kentucky: A Random Sequential Mechanism of Aminoglycoside Acetylation by Mycobacterium tuberculosis Eis Protein.
- Wagner Laboratory, Harvard Medical School:
- Structure-activity relationship study of 4EGI-1, small molecule eIF4E/eIF4G protein-protein interaction inhibitors.
- Perspectives in magnetic resonance: NMR in the post-FFT era.
- Wang Laboratory, Academia Sinica: Linked Production of Pyroglutamate-Modified Proteins via Self-Cleavage of Fusion Tags with TEV Protease and Autonomous N-Terminal Cyclization with Glutaminyl Cyclase In Vivo.
- Wolberger Laboratory, Johns Hopkins U School of Medicine: New insights into ubiquitin E3 ligase mechanism.
- Yu Laboratory, U Texas Southwestern Medical Center: Structural insights into the TRIM family of ubiquitin E3 ligases.
- Zheng Laboratory, U Washington: Plant ubiquitin ligases as signaling hubs.
- Zimmer Laboratory, U Virginia School of Medicine: Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP.
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.