Dear Consortium Members and Affiliates,
And we're off. September is at its end and the pace has quickened around the Harvard campus. Here at SBGrid there's lots of new going on - the launch of our new website, a new version of our laptop installation script, new grant funding - along with our usual items of note: webinar updates, a glimpse into Doug Daniels's lab at the Broad Institute, six new SBGrid citations, several software updates, and three new members.
The new SBGrid website was launched a few days ago. We're still working out a few kinks, but are excited to have a new layout with improved functionality. Please take a moment to browse around and let us know what you think.
In conjunction with the new website, SBGrid also set up a new support forum where you can find quick answers to commonly asked questions. We encourage you to join or start a new discussion thread on any topic relevant to structural biologists. You can access the forum here or from the /Get Help/Support Forum link on our website.
We've recently finished a new version of our laptop installation script, which, true to it's name, will allow you to install a subset of the SBGrid software collection on your laptop. Follow these instructions to get started and contact us at email@example.com with any questions.
New grant funding just came our way from the NSF that will allow us to build some new tools for members and contributing developers. Our bibliography builder will make the chore of software citation as simple as a few clicks. Using our web interface, authors will be able to select the software titles used in their work and receive a complete list of relevant citations. With new software tracking scripts we also aim to provide developers with much needed information on how their applications are used. We'll keep you posted on the development of these new tools.
In webinar news, we just finished a two-parter featuring Christian Olsen, who demonstrated sequence analysis and molecular cloning functionality in the Geneious application. Part I of his webinar has already been posted to the SBGrid YouTube channel under the "Other Tools" playlist, and Part II will soon be added. While visiting be sure to take a look at some of the 40+ other videos we've posted, including the popular PyMOL (3100 views) and SAXS (2176 views) presentations.
In this month's SBGrid Tale we talked to Doug Daniels at the Broad Institute. Daniels has spent the last two years building a new protein science group at the Broad, focused on discovering new drugs for targets previously thought undruggable.
Citations for SBGrid's eLife paper recently appeared in publications from several member labs, including those of Titus Boggon (Yale), Catherine Drennan (MIT), Christopher Fromme (Cornell), Thomas Schwartz (MIT), Holger Sondermann (Cornell), and Navtej Toor (UC San Diego). Our special highlight for September goes to Navtej Toor for his Nature publication "Crystal structure of a eukaryotic group II intron lariat". A list of these and a selection of publications from other members are included below.
We just pushed out several software updates, including new versions of BUSTER, CCP4, EMAN2, Gromacs, MODELLER, PyMOL, and Schrodinger. Additional details are included in the software changes section below.
Three new members joined SBGrid during the month of September: Sebastian Klinge joined a growing group from Rockefeller University, Genaro Ramirez Correa became our fourth member at Johns Hopkins University School of Medicine, and we have one new institute to add to our member map, with the addition of Ramachandran Murali from Cedars-Sinai. Welcome to our new members!
With the release of version 3.4.2, 2dx has had it's first upgrade in two years. This version includes many new features, including support for OSX 10.9 and 2d difference mapping, and goes after bugs, fixing many and creating a new tool to track them down.
BUSTER version 2.10.2 was pushed out this month. This update includes many improvements and fixes along with several new tools: Rhofit, buster-report, and Pipedream.
CCP4 6.4.0 was updated to include patches 20 and 21, which correct an OMP problem, allow an update to the new MrBUMP, and fix a maddening XDS-Pointless assertion error bug.
The latest from EMAN2, now at version 2.1, brings big improvements in stability and the addition of e2refine_easy, a primary single particle refinement program. Other enhancements include a new 3-D viewer and conversion options for Relion or Frealign for comparative refinement.
Many improvements were added to version 5.0 of Gromacs. Major changes were made in the analysis tools and the developers have posted a tip sheet here on how to translate old habits to new.
MODELLER version 9.14 fixes a number of bugs and most notably adds support for the new PDB format.
PyMOL was updated to version 18.104.22.168, which fixes an issue with volume carving.
Schrodinger 2014-3 includes improvements to the Maestro GUI and new tight core constraints for Glide -ligand and -induced fit docking.
Included below is a selection of publications that have appeared from Consortium member laboratories over the past 30 days. For the full list of publications please visit the Member Publications page on the SBGrid website.
In last month's newsletter we mistakenly attributed a couple of publications to the wrong authors due to a wrinkle in one of our scripts that we're still ironing out. Please accept our apologies for this mistake and any confusion that may have resulted.
- Karen Anderson's Group, Yale University School of Medicine: Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase-dihydrofolate reductase.
- Axel Brunger's Group, Standford U: Deformable elastic network refinement for low-resolution macromolecular crystallography.
- Amedeo Caflisch's Group, U Zurich:
- High-resolution visualisation of the States and pathways sampled in molecular dynamics simulations.
- A molecular simulation protocol to avoid sampling redundancy and discover new states.
- James Chou's Group, Harvard Medical School: Fatty Acid flippase activity of UCP2 is essential for its proton transport in mitochondria.
- Kevin Corbett's Group, U California San Diego: Sister kinetochores are mechanically fused during meiosis I in yeast.
- Michael Cosgrove's Group, SUNY Upstate Medical U: Characterization of the Grp94/OS-9 Chaperone-Lectin Complex.
- Brian Crane's Group, Cornell U: Photochemistry of flavoprotein light sensors.
- Sean Crosson's Group, U Chicago: The Brucella abortus virulence regulator, LovhK, is a sensor kinase in the general stress response signaling pathway.
- Catherine Drennan's Group: MIT: Crystallographic evidence for drastic conformational changes in the active site of a flavin-dependent N-hydroxylase.
- Victoria D'Souza's Group, Harvard U: A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing.
- Adrian Ferré-D'Amaré's Group, NIH: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
- Juan Fontecilla-Camps's Group, IBS Grenoble: Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan.
- Craig Lindsley's Group, Vanderbilt U:
- 2013 Philip S. Portoghese Medicinal Chemistry Lectureship: Drug Discovery Targeting Allosteric Sites.
- Discovery of a Highly Selective PLD2 Inhibitor (ML395): A New Probe with Improved Physiochemical Properties and Broad-Spectrum Antiviral Activity against Influenza Strains.
- James Hurley's Group, U California Berkeley: Insights into β2-adrenergic receptor binding from structures of the N-terminal lobe of ARRDC3.
- Martin Jinek's Group, U Zurich: Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease.
- Tom Kirchhausen's Group, Boston Children's Hospital: Dynamin recruitment and membrane scission at the neck of a clathrin-coated pit.
- Sriram Krishnaswamy's Group, U Penn: New insights into the spatiotemporal localization of prothrombinase in vivo.
- John Kuriyan's Group, U California Berkeley: Emerging concepts in the regulation of the EGF receptor and other receptor tyrosine kinases.
- Peter Kwong's Group, NIH: Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface.
- Andres Leschziner's Group, Harvard University: Traffic control: adaptor proteins guide dynein-cargo takeoff.
- Galina Lepesheva's Group, Vanderbilt U: Sequence variation in CYP51A from the Y strain of Trypanosoma cruzi alters its sensitivity to inhibition.
- John Markley's Group, U Wisconsin-Madison: PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.
- Lawrence Marnett's Group: Vanderbilt U: Protein Modification by Adenine Propenal.
- Wayne Marasco's Group, Dana-Farber Cancer Institute: Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on SARS-Coronavirus Neutralization Escape and Fitness.
- Yorgo Modis's Group, Yale U: An inheritable variant of the innate immune receptor MDA5 promotes clearance of hepatitis C virus.
- Dinshaw Patel's Group, Memorial Sloan Kettering Cancer Center:
- Binding-Pocket and Lid-Region Substitutions Render Human STING Sensitive to the Species-Specific Drug DMXAA.
- The evolutionary journey of Argonaute proteins.
- George Phillips's Group, Rice U: Structure and Substrate Specificity of a Eukaryotic Fucosidase from Fusarium graminearum.
- Anna Pyle's Group, Yale U:
- The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain.
- The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus.
- Tom Rapoport's Group, Harvard Medical School: Key Steps in ERAD of Luminal ER Proteins Reconstituted with Purified Components.
- Douglas Rees's Group, California Institute of Technology:
- The Structure of a Conserved Piezo Channel Domain Reveals a Topologically Distinct β Sandwich Fold.
- Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase.
- Chuck Sanders's Group, Vanderbilt U: Homology Model of PMP22 Suggests Mutations Resulting In Peripheral Neuropathy Disrupt Transmembrane Helix Packing.
- Michael Sattler's Group, Institute of Structural Biology: Structural basis for the assembly of the Sxl-Unr translation regulatory complex.
- Celia Schiffer's Group, U Massachusetts Medical School: Structural Analysis of Asunaprevir Resistance in HCV NS3/4A Protease.
- Frank Sicheri's Group, U Toronto: Dimerization-induced allostery in protein kinase regulation.
- Piotr Sliz's Group, Harvard Medical School: Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4).
- Joseph Sodroski, Dana-Farber Cancer Institute: Contribution of glutamine residues in the helix 4-5 loop to capsid-capsid interactions in simian immunodeficiency virus of macaques.
- Holger Sondermann's Group, Cornell U: Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP.
- Michael Stone's Group, Vanderbilt U: Major Groove Orientation of the (2S)-N6-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene.
- Niraj Tolia's Group, Washington U School of Medicine: Critical Glycosylated Residues in Exon Three of Erythrocyte Glycophorin A Engage Plasmodium falciparum EBA-175 and Define Receptor Specificity.
- Navtej Toor's Group, U California San Diego: Crystal structure of a eukaryotic group II intron lariat.
- Gerhard Wagner's Group: Harvard Medical School: NMR resonance assignments of the catalytic domain of human serine/threonine phosphatase calcineurin in unligated and PVIVIT-peptide-bound states.
- Ronnie Wei's Group, Sanofi/Genzyme: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGFβ reveal structural plasticity of antibody-antigen interactions.
- Cynthia Wolberger's Group, Johns Hopkins U School of Medicine: Alternate deacylating specificities for the archaeal sirtuins Sir2Af1 and Sir2Af2.
- Hao Wu's Group, Boston Children's Hospital: IRAK4 Dimerization and trans-Autophosphorylation Are Induced by Myddosome Assembly.
- Kai Wucherpfennig's Group, Dana-Farber Cancer Institute: Molecular mechanisms for contribution of MHC molecules to autoimmune diseases.
- Hongtao Yu's Group, U Texas Southwestern Medical Center: Genome-wide siRNA screen reveals coupling between mitotic apoptosis and adaptation.
- Chloe Zubieta, Institute of Life Sciences Research and Technologies: Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis.
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software.
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.