Dear Consortium Members and Affiliates,
Bing, bang, bop! It's once again time for the SBGrid newsletter, as February careens to stop. Things at SBGrid are moving at a vigorous clip, with an expanded program for the June Computing School, the availability of new computational resources through XSEDE, a software release that includes 2 new applications and 9 updates, a 2-part SAX webinar on tap for March, and a look at Frank Delaglio, of NMRPipe fame, and the unconventional path he followed to his dream career.
Time to refresh your data processing skills! Most crystallographers have read a recent paper by Karplus and Diederichs on Pearson's Correlation coefficient (Science, 336:1030-3), yet many of us are not sure how to apply these statistics to routine data processing and structural determination problems. Kay Diederichs will be one of the key speakers presenting at the SBGrid/NE-CAT Computing School in Boston, which is scheduled to take place June 5-7th. The workshop will include a special panel discussion on Table I statistics and numerous presentations by leading software developers, including CCP4, Phenix, and HKL. Please do not miss this opportunity to visit us in Boston and meet with the SBGrid team.
For out-of-towners, we've created a mailing list to help you connect with others looking to share rides or double up on rooms.
A limited number of 15-min trainee presentation slots are available for the Saturday session, so please be sure to submit your abstracts to Michelle at firstname.lastname@example.org no later than March 10th. Selected applicants will receive a $500 travel award.
The Extreme Science and Engineering Discovery Environment (XSEDE) integrates several high performance national computational facilities in the US. Jason Key has taken on the role of XSEDE Campus Champion for SBGrid. Members interested in accessing XSEDE computational resources should email email@example.com with a request to be added to the SBGrid XSEDE mailing list. Jason will moderate the list, which will act as a forum for members to discuss topics specific to structural biology computations on XSEDE, and will include information about XSEDE resources and the application process for pilot allocation and utilization of Campus Champion startup time.
February's software release includes updates to Schrodinger, CCP4, Relax, Bsoft, Jalview, ATSAS, MOSFLM, iMosflm, and Modeller, as well as two new applications: PDB_Redo and Hydropro.
We had a great turnout for Wladek Minor's presentation on HKL2000 in February, and in March we are looking forward to a two-part SAXS tutorial presented by Thomas Grant from Eddie Snell's lab at the Hauptman-Woodward Institute. Due to a scheduling snafu, our March webinar won't be live, but we'll make an announcement to members once it is posted to our YouTube channel.
For our February tale, we're continuing our focus on software developers with a story featuring Frank Delaglio, who describes how his interest in science was sparked at the age of seven.
Alexandre Bonvin from University Utrecht is the newest SBGrid member. Welcome Alexandre!
Linux 64-bit and OS X Intel
Schrodinger has been updated to version 2013-3. The 2014-1 release should be available in a week or so.
Modeller is now running at version 9.13. This one is mostly bug fixes.
ATSAS has been updated to version 2.5.2. The ATSAS web forum has a list of the changes.
Bsoft has been updated to version 1.8.8. The Bsoft web site has documentation and tutorials for this application.
Relax has been updated to version version 3.1.5.
Jalview version 2.8.0b1 has been installed. This is a bug fix release in preparation for the major 3.0 release later this year.
MOSFLM and iMosflm have been updated to version 7.1.0. We're gently twisting Harry Powell's arm to do a webinar on the latest MOSFLM awesomeness, which include multiple lattice processing and parallel integration runs on Mac and Linux. The iMosflm graphical interface for MOSFLM includes support for these new features and a long list of additional features and bugfixes. More details on using these new features are available on the iMosflm home page.
CCP4 6.4.0 patch 8 has been installed. The CCP4 updates are primarily bugfixes.
PDB_Redo version 5.31 is now installed. This is Robbie Joosten's PDB validation pipeline that incorporates multiple tools for testing multiple facets of your PDB for correctness. The How does it work page describes the process in detail.
Hydropro version 10 has been installed. This tool "computes the hydrodynamic properties of rigid macromolecules (proteins, small nucleic acids, macromolecular complexes, etc.) from their structure". A full user guide is available on the Hydropro home page.
Since our last newsletter, the following publications have appeared from Consortium member labs:
- Adams Lab, UChicago: Lipid presentation by human CD1 molecules and the diverse T cell populations that respond to them.
- Allingham Lab, Queen's U: An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.
- Amarasinghe Lab, WashingtonU St Louis: In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity.
- Anderson Lab, YaleU School of Medicine: Virtual screening reveals allosteric inhibitors of the Toxoplasma gondii thymidylate synthase-dihydrofolate reductase.
- Ban Lab, ETH Zurich: A new system for naming ribosomal proteins.
- Berger Lab, Johns Hopkins Medical Institute: Fluoroquinolone-Gyrase-DNA Complexes: Two Modes of Drug Binding.
- Bjorkman Lab, CalTech:
- Structural Insights on the Role of Antibodies in HIV-1 Vaccine and Therapy.
- Electron tomography of HIV-1 infection in gut-associated lymphoid tissue.
- Blobel Lab, RockefellerU: Structure of a myosinbulletadaptor complex and pairing by cargo.
- Boggon Lab, YaleU School of Medicine:
- Tyr Phosphorylation of PDP1 Toggles Recruitment between ACAT1 and SIRT3 to Regulate the Pyruvate Dehydrogenase Complex.
- Cerebral cavernous malformation proteins at a glance.
- Bradner Lab, Dana-Farber Cancer Institute:
- Regulation of MYC Expression and Differential JQ1 Sensitivity in Cancer Cells.
- RapidCaP, a Novel GEM Model for Metastatic Prostate Cancer Analysis and Therapy, Reveals Myc as a Driver of Pten-Mutant Metastasis.
- Caflisch Lab, UZurich: A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods.
- Chazin Lab, VanderbiltU:
- Divergent Regulation of RyR2 Calcium Release Channels by Arrhythmogenic Human Calmodulin Missense Mutants.
- Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A.
- Crosson Lab, UChicago: A cell cycle and nutritional checkpoint controlling bacterial surface adhesion.
- Davies Lab, Queen's U:
- An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.
- Determining the Ice-binding Planes of Antifreeze Proteins by Fluorescence-based Ice Plane Affinity.
- Doudna Lab, UC Berkeley:
- Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation.
- DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.
- Fesik Lab, VanderbiltU: Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A.
- Garcia Lab, StanfordU: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis.
- Heras Lab, La Trobe U: Targeting Virulence not Viability in the Search for Future Antibacterials.
- Hoelz Lab, CalTech: Evidence for an evolutionary relationship between the large adaptor nucleoporin Nup192 and karyopherins.
- Ikura Lab, U Toronto:
- The RhoGEF GEF-H1 Is Required for Oncogenic RAS Signaling via KSR-1.
- p120RasGAP Is a Mediator of Rho Pathway Activation and Tumorigenicity in the DLD1 Colorectal Cancer Cell Line.
- Integrated RAS signaling defined by parallel NMR detection of effectors and regulators.
- Jardetzky Lab, StanfordU School of Medicine: Activation of paramyxovirus membrane fusion and virus entry.
- Jia Lab, Queen's U:
- Structural Analysis and Identification of PhuS as a Heme-Degrading Enzyme from Pseudomonas aeruginosa.
- Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe2+-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli.
- Kvansakul Lab, La Trobe U: Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission.
- Kwong Lab, NIH/NIAID:
- Antibodies VRC01 and 10E8 Neutralize HIV-1 with High Breadth and Potency Even with Ig-Framework Regions Substantially Reverted to Germline.
- Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.
- Lambright Lab, UMass Medical School: Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM.
- Lima Lab, MSKCC: The eukaryotic RNA exosome.
- Lindsley Lab, VanderbiltU:
- A Duplexed High-Throughput Screen to Identify Allosteric Modulators of the Glucagon-Like Peptide 1 and Glucagon Receptors.
- Novel GlyT1 inhibitor chemotypes by scaffold hopping. Part 2: Development of a [3.3.0]-based series and other piperidine bioisosteres.
- Novel GlyT1 inhibitor chemotypes by scaffold hopping. Part 1: Development of a potent and CNS penetrant [3.1.0]-based lead.
- Antipsychotic Drug-Like Effects of the Selective M4 Muscarinic Acetylcholine Receptor Positive Allosteric Modulator VU0152100.
- Luger Lab, Colorado StateU: Editorial overview: Nucleic acid movers and shakers.
- Mackinnon Lab, RockefellerU: Mechanosensitivity is mediated directly by the lipid membrane in TRAAK and TREK1 K+ channels.
- Moazed Lab, Harvard Medical School: Determinants of Heterochromatic siRNA Biogenesis and Function.
- Modis Lab, YaleU: Relating structure to evolution in class II viral membrane fusion proteins.
- Patel Lab, MSKCC:
- A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer.
- SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.
- Arabidopsis Accelerated Cell Death 11, ACD11, Is a Ceramide-1-Phosphate Transfer Protein and Intermediary Regulator of Phytoceramide Levels.
- Reinisch Lab, YaleU School of Medicine: Legionella pneumophila subversion of host vesicular transport by SidC effector proteins.
- Richmond Lab, ETH Zurich: Structure of the full-length yeast Arp7-Arp9 heterodimer.
- Schlessinger Lab, Yale U School of Medicine: Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers.
- Sharpe Lab, Hospital for Sick Children: The mechanism of membrane disruption by cytotoxic amyloid oligomers formed by PrP(106-126) is dependent on bilayer composition.
- Sicheri Lab, UToronto: Dimeric Structure of Pseudokinase RNase L Bound to 2-5A Reveals a Basis for Interferon-Induced Antiviral Activity.
- Skiniotis Lab, UMichigan: Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system.
- Sodroski Lab, Dana-Farber Cancer Institute:
- Loss of a conserved N-linked glycosylation site in the SIV envelope glycoprotein V2 region enhances macrophage tropism by increasing CD4-independent cell-to-cell transmission.
- Contribution of PDZD8 to Stabilization of the Human Immunodeficiency Virus (HIV-1) Capsid.
- Sosnick Lab, UChicago: Factors That Control the Chemistry of the LOV Domain Photocycle.
- Stern Lab, UMass Medical School: HLA-DM and HLA-DO, key regulators of MHC-II processing and presentation.
- Wagner Lab, Harvard Medical School: 3-Substituted Indazoles as Configurationally Locked 4EGI-1 Mimetics and Inhibitors of the eIF4E/eIF4G Interaction.
- Walz Lab, Harvard Medical School: A requirement for ER-derived COPII vesicles in phagophore initiation.
- Wang Lab, Academia Sinica:
- TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins.
- Structural insights into the catalytic mechanism of human squalene synthase.
- Wucherpfennig Lab, Dana-Farber Cancer Institute:
- Polarized release of T-cell-receptor-enriched microvesicles at the immunological synapse.
- In vivo discovery of immunotherapy targets in the tumour microenvironment.
- Yu Lab, UT Southwestern: A protective chaperone for the kinetochore adaptor bub3.
- Yudin Lab, UToronto:
- Development of the Direct Suzuki-Miyaura Cross-Coupling of Primary B-Alkyl MIDA-boronates and Aryl Bromides.
- Air- and Moisture-Stable Amphoteric Molecules: Enabling Reagents in Synthesis.
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.