Dear Consortium Members and Affiliates,
Welcome to the Celebrate Boston Red Sox! edition of the SBGrid newsletter. In today's newsletter you can read about Linux workstations for Structural Biology, Geneious software, 15 new software updates, and a little history about scientist-developer Jane Richardson. Also don't forget to visit our YouTube/SBGridTV channel to view the most recently added software tutorials and tune in for our upcoming NMR webinars. After 6 nail-biting nights, we are happy to say Congratulations Red Sox!
Many of you have asked for recommendations when buying new workstations. In response, we have designed recommended configurations for standard workstations and 3d stereo workstations. You can see the details for each of these configurations on the Thinkmate website, where you can purchase directly or use the specs for a template to purchase through your institution's preferred vendor. We are planning to announce recommendations for additional systems, including a GPU workstation and a high density processing node, in the November newsletter.
Our Geneious software license has now transitioned from the unlimited trial license to our own limited-seat license. Based on the initial trial period, our current license should meet demand, but we can continue to tweak some settings if there are issues with accessing the software, so please be sure to send us feedback if you encounter any problems.
Jane Richardson, from Duke University, is the subject of our October Tale. Jane talked with us about how her early work drawing structures by hand gave her an intuitive sense for proteins that provided the foundation for her work on structure validation and the development of MolProbity.
For the next two months our webinars will focus on NMR applications. In November we will hear from Frank Delaglio on the 7th and the 14th, first with a review of spectral processing concepts and then with an overview of how to use NMRPipe to understand spectroscopic data. A presentation by Homay Valafar on his application REDCAT, a residual dipolar coupling analysis tool, will follow on December 5th.
We have two new members this month, both hailing from the University of Maryland School of Medicine: Eric Sundberg and Marzena Pazgier. Welcome to our new members!
Software Update
Since our last newsletter we have installed software updates for Rosetta, HKL2MAP, IMOD, PHENIX, Xmipp, HKL2000, xia2, HOLE, NMRPipe, Mole, Schrodinger, Desmod, HKL2000, and two new applications were added to the collection: Geneious and Gorgon.
Notable Software Changes
Geneious, the newly added software for bioinformatic analysis, was updated to version R7, which includes seven major new features. Users can now 1) create and share data analysis workflows, 2) use the Gibson assembly method for one-step cloning of fragments (automated primer design and batch cloning/shuffling are supported), 3) perform codon optimization, 4) carry out one-step TOPO cloning of fragments into a vector, 5) copy and paste annotations, 6) use new visualization of coverage in sequence alignment, and 7) use new plugins for tree building and viewing and for alignment.
Schrodinger and Desmond software for macromolecular modeling were upgraded to 2013-2 release. Dozens of usability and performance improvements are documented on the Schrodinger website: http://www.schrodinger.com/downloads/NewFeatures/NewFeatures_2013-2.pdf. The most notable changes include new simulation interactions diagrams to analyze protein-ligand interactions and geometries over the course of MD simulations, expansion of high-quality parameters for Jaguar pKa to 19 additional functional groups, updated core-hopping libraries, and support for KNIME 2.8.
For crystallographers, we have updated two data processing applications, HKL2000 and xia2. No details are provided for the new version of HKL2000 (704w), but typically the newer versions are extended to include additional detector support. The new version of xia2 includes support for CCP4 version 6.4. We are currently compiling this new version of CCP4 and will have it ready for release in November. The newly installed version of Phenix (1.8.4 ) fixed several bugs from the September release.
For electron microscopists, we have added the application Gorgon, an interactive molecular modeling system that supports protein backbone tracing, secondary structure identification, visualization and other modules. Gorgon is the result of a collaboration between Washington University in St. Louis and Baylor College of Medicine. Gorgon's website is difficult to see on our screens (dark grey font on black background) but it contains several useful training videos. We have also installed a newer and faster version of XMIPP and a new version of the application IMOD.
No upgrade information was provided for NMRPipe, but please tune in to our NMR Webinars with Frank Delaglio, which are scheduled for November 7th and 14th. This most recent release of NMRPipe replaced the January 2013 version of the software.
Publications
Since our last newsletter, the following publications have appeared from Consortium member labs:
- Allingham Lab, Queen's U: Role of Ca2+ in folding the tandem β-sandwich extender domains of a bacterial ice-binding adhesin.
- Anderson Lab, Yale: First Three-Dimensional Structure of Toxoplasma gondii Thymidylate Synthase-Dihydrofolate Reductase: Insights for Catalysis, Interdomain Interactions, and Substrate Channeling.
- Baxter Lab, Yale: A β-Boronopeptide Bundle of Known Structure As a Vehicle for Polyol Recognition.
- Beese Lab, Duke: Visualization of Synaptic Inhibition with an Optogenetic Sensor Developed by Cell-Free Protein Engineering Automation.
- Blobel Lab, RockefellerU: Structure and nucleic acid binding activity of the nucleoporin Nup157.
- Bradner Lab, Dana-Farber Cancer Institute: Efficacy of BET Bromodomain Inhibition in Kras-Mutant Non-Small Cell Lung Cancer.
- Brunger Lab, StanfordU: Complexin-1 Enhances the On-Rate of Vesicle Docking via Simultaneous SNARE and Membrane Interactions.
- Caflisch Lab, UZurich: Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics.
- Chazin Lab, Vanderbilt U: Surface Reengineering of RPA70N Enables Cocrystallization with an Inhibitor of the Replication Protein A Interaction Motif of ATR Interacting Protein.
- Davies Lab, Queen's U: Role of Ca2+ in folding the tandem β-sandwich extender domains of a bacterial ice-binding adhesin.
- Doudna Lab, UC Berkeley: Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.
- Drennan Lab, MIT: X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry.
- Eichman Lab, VanderbiltU: Depurination of N7-Methylguanine by DNA Glycosylase AlkD Is Dependent on the DNA Backbone.
- Garcia Lab, Stanford:
- Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody.
- Human LilrB2 is a β-amyloid receptor and its murine homolog PirB regulates synaptic plasticity in an Alzheimer's model.
- Jia Lab, QueensU: Detergent quantification in membrane protein samples and its application to crystallization experiments.
- Lepsheva Lab, VanderbiltU: Design or screening of drugs for the treatment of Chagas disease: what shows the most promise?
- Lindsley Lab, VanderbiltU:
- Octahydropyrrolo[3,4-c]pyrrole negative allosteric modulators of mGlu1.
- Glycine Transporter-1 Inhibition Promotes Striatal Axon Sprouting via NMDA Receptors in Dopamine Neurons.
- Exploration of Allosteric Agonism Structure-Activity Relationships within an Acetylene Series of Metabotropic Glutamate Receptor 5 (mGlu5) Positive Allosteric Modulators (PAMs): Discovery of 5-((3-Fluorophenyl)ethynyl)-N-(3-methyloxetan-3-yl)picolinamide (ML254).
- 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.
- Kornberg Lab, Standford: Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex.
- Rapoport Lab, Harvard Medical School: Structure of the SecY channel during initiation of protein translocation.
- Schlessinger Lab, Yale U School of Medicine: Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.
- Shapiro Lab, ColumbiaU: De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts.
- Sodroski Lab, Dana-Farber Cancer Institute: Selection of Low Envelope Glycoprotein Reactivity to Soluble CD4 and Cold During Simian-Human Immunodeficiency Virus Infection of Rhesus Macaques.
- Stone Lab, VanderbiltU:
- Ring-Opening of the γ-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4.
- Site-Specific Stabilization of DNA by a Tethered Major Groove Amine, 7-Aminomethyl-7-deaza-2'-deoxyguanosine.
- Wang Lab, Academia Sinica: Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor.
- Wucherpfennig Lab, Dana-Farber Cancer Institute: Crossreactivity of a human autoimmune TCR is dominated by a single TCR loop.
- Zheng Lab, UWashington: Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.
- Zimmer Lab, UVirginia School of Medicine: BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis.
- Zheng Lab, UWashington: Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.
- Zoltowski, Southern Methodist U: Blue Light-Induced Dimerization of a Bacterial LOV-HTH DNA-Binding Protein.
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.