Dear Consortium Members and Affiliates,
We've been busy digging out the past couple of days and now, with the obligatory blizzard behind us, have some January news to pass along. We have a date for the February iMosflm webinar, a story on Martin Jinek from the University of Zurich, a software push that includes several updates and one new application, a note about CCP4 and Coot, and 6 new members to welcome.
In webinar news, we just posted Pawel Penczek's webinar on the challenges of single particle EM structure determination to our YouTube channel. Next in line is a presentation by Dr. Harry Powell from the MRC Laboratory of Molecular Biology, on iMosflm - a tool for data reduction.
Our January webtale features Martin Jinek, Assistant Professor from the University of Zurich. While his lab has a strong focus on the development of CRISPR technology, Jinek emphasizes his roots and continuing studies in basic science: the "chemical basis of life still fascinates me and drives my career.” Read the full story here.
January's software push includes new releases for Biopython, CCP4, EMAN2, Jalview, NMRPipe, and VMD and we have added iPython Notebook to our collection. More details are included in the Software Changes section below.
A note about Coot: Coot is now rolled into the default CCP4 installation, which means that users will now access the version of Coot (currently 0.8.1) available in the CCP4 package. If you wish to access a different version of Coot, please email bugs@sbgrid.org for instructions.
We have six new members to welcome for the month of January. Brian Kelch has become our fifth member from the University of Massachusetts Medical School, Janice Robinson our seventh from the University of Iowa, Andrew McCarthy and Stephen Cusack have joined from EMBL Grenoble, and we have our first members representing India: Ramaswamy Subramanian and Arati Ramesh from the National Centre for Biological Sciences, Bangalore. Welcome to our new members!
Software Changes
Biopython was updated to version 1.64. This version includes Bio.CodonAlign, a new experimental module that facilitates building codon alignment, new tree construction and consensus modules for Bio.Phylo, automatic downloads of NCBI DTD files for XML parsing in Bio.Entrez, support for Python 2.6, 2.7, 3.3, and 3.4, and a number of other improvements.
CCP4 had a big update to version 6.5. This release includes numerous updates and several new programs, including Privateer-validate, Feckless, chemoinformatics support for Refmac in the form of Acedrg v90 and LibG, Blend v0.5.10, and Crank-2.
In EMAN2's latest -- version 2.1 -- the developers proclaim no more BDB! and note improvements in ease-of-use, better infrastructure for single particle tomography, and gold-standard resolution for refinements with automatic filtration. They also note that version 2.1 files are not backwards compatible and that 2.0x files will need conversion.
iPython Notebook was added as a stand-alone application. iPython notebook is a web-based interactive computational environment that allows you to combine code execution, text, mathematics, plots, and rich media into a single document.
Jalview version 2.8.2 is now part of our default installation. This update includes an option to color RNA and protein secondary structures, improvements to pairwise alignment, new options for RNA pseudoknot annotation, along with many other improvements and bug fixes.
NMRPipe is now at version 20140803. No additional information is available.
VMD was updated to version 1.9.2, which includes a new built-in TachyonL-OptiX GPU-accelerated ray tracing engine, support for off-screen OpenGL rendering, and improvements to QuickSurf.
Publications
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.
- Amir Khan's Group, Trinity College Dublin: PD-L1(hi) B cells are critical regulators of humoral immunity.
- Guy Schoehn's Group, Institut de Biologie Structurale, Grenoble: PscI is a type III secretion needle anchoring protein with in vitro polymerization capacities.
- Joseph Schlessinger's Group, Yale U School of Medicine: Heparin is an activating ligand of the orphan receptor tyrosine kinase ALK.
- James Chou's Group, Harvard Medical School: Mapping Conformational Heterogeneity of Mitochondrial Nucleotide Transporter in Uninhibited States.
- Filippo Mancia's Group, Columbia U: Native Serotonin 5-HT2C Receptors are Expressed as Homodimers on the Apical Surface of Choroid Plexus Epithelial Cells.
- Walther Chazin's Group, Vanderbilt U: Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress.
- Gerhard Wagner's Group, Harvard Medical School: Force-dependent transition in the T-cell receptor β-subunit allosterically regulates peptide discrimination and pMHC bond lifetime.
- Ron Rock's Group, U Chicago: Pharmacological activation of myosin II paralogs to correct cell mechanics defects.
- Christopher Garcia's Group, Stanford U: Self-Determination in the T Cell Repertoire.
- Chris Fromme's Group, Cornell U: Membrane Trafficking: Licensing a Cargo Receptor for ER Export.
- David Wilson's Group, La Trobe U: Effects of the electronic structure of five-membered N-heterocyclic carbenes on insertion of silanes and boranes into the NHC C-N bond.
- Hongtao Yu's Group, U Texas Southwestern Medical School: Multiple assembly mechanisms anchor the KMN spindle checkpoint platform at human mitotic kinetochores.
- Melanie Ohi's Group, Vanderbilt U: Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements.
- James Bradner's Group, Dana-Farber Cancer Institute: MLL partial tandem duplication leukemia cells are sensitive to small molecule DOT1L inhibition.
- Rachelle Gaudet's Group, Harvard University: Insights into the molecular foundations of electrical excitation.
- John Williams's Group, City of Hope: Development of a High Affinity, Non-covalent Biologic to Add Functionality to Fabs.
- Georgios Skiniotis's Group, U Michigan: A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation.
- Amedeo Caflisch's Group, U Zurich: Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations.
- Hazel Holden's Group, U Wisconsin-Madison: New Role for the Ankyrin Repeat Revealed by a Study of the N-Formyltransferase from Providencia alcalifaciens.
- Joseph Sodroski's Group, Dana-Farber Cancer Institute: Infection of monkeys by simian-human immunodeficiency viruses with transmitted/founder clade C HIV-1 envelopes.
- David Wilson's Group, La Trobe U: The Fate of NHC-Stabilized Dicarbon.
- Theodore Jardetzky's Group, Stanford U: On the stability of parainfluenza virus 5 F proteins.
- Michael Stone's Group, Vanderbilt U: DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
- Axel Brunger's Group, Stanford U: Mechanistic insights into the recycling machine of the SNARE complex.
- Andreas Plueckthun's Group, U Zurich: Phase Behavior of a Designed Cyclopropyl Analogue of Monoolein: Implications for Low-Temperature Membrane Protein Crystallization.
- Jens Meiler's Group, Vanderbilt U: CASP10 - BCL::Fold efficiently samples topologies of large proteins.
- Theodore Jardetzky's Group, Stanford U: Membrane Anchoring of Epstein-Barr Virus gp42 Inhibits Fusion with B Cells Even with Increased Flexibility Allowed by Engineered Spacers.
- Brian Zoltowski's Group, Southern Methodist U: Structural Biochemistry of a Fungal LOV Domain Photoreceptor Reveals an Evolutionarily Conserved Pathway Integrating Light and Oxidative Stress.
- Andreas Plueckthun's Group, U Zurich: Designed Ankyrin Repeat Proteins (DARPins): Binding Proteins for Research, Diagnostics, and Therapy.
- Michael Cosgrove's Group, SUNY Upstate Medical U: Biochemical Reconstitution and Phylogenetic Comparison of Human SET1 Family Core Complexes Involved in Histone Methylation.
- Peter Davies Group, Queen's U: Flies expand the repertoire of protein structures that bind ice.
- Anna Pyle's Group, Yale U: Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells.
- James Berger's Group, Johns Hopkins University: Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement.
- Alexandre Bonvin's Group, Utrecht U: Information-Driven Modeling of Protein-Peptide Complexes.
- Danesh Moazed's Group, Harvard Medical School: RNA-mediated epigenetic regulation of gene expression.
- Peter Kwong's Group, NIH: Correction for Acharya et al., Heavy Chain-Only IgG2b Llama Antibody Effects Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes Elements of Coreceptor- and CD4-Binding Sites.
- Pamela Bjorkman's Group, California Institute of Technoology: Not Second Class: The First Class II MHC Crystal Structure.
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.