Dear Consortium Members and Affiliates,
The winter solstice (for those of us in the Northern Hemisphere) is just a day away and it's a relief to anticipate a few more minutes of sunlight each day. As 2013 comes to a close we have a new lineup of webinars, GPU workstation recommendations, a profile on Peter Kwong and his work at the NIH Vaccine Research Center, and a small software update.
SBGrid staff will be on holiday from December 24th through January 1st, thanks to Harvard's generous holiday schedule. We'll keep our eyes open for emergencies during the week, but the small stuff will be hold. Happy Holidays to all and see you in the New Year!
Our webinar schedule for 2014 is starting to shape up. We'll take a break in January, but will launch the series on February 6th with a presentation from Wladek Minor on HKL2000. Also on the calendar are presentations on Phenix-Rosetta refinement and the Gorgon molecular modeling application.
If you're in the market for a high-performance computer, we've added recommendations for a GPU-enabled workstation to the Thinkmate website. As always, we suggest that you consult your institutional IT department before making any computer purchases, since they might have a preferred vendor or limitations on hardware they can support.
Peter Kwong is the subject of our December member tale. You can read about his entry into HIV research and his mid-western approach to vaccine development here.
We also have two new publications from our members citing SBGrid: Qing Fan from Columbia University communicates in Nature on ligand activation in human GABAB receptor and Prof. Suzanne Walker, from Harvard Medical School, reports in Science on Cys-Glu cleavage by OGT glycosyltransferase.
Eleven new members from two new institutions joined SBGrid since our last newsletter. Marcos Sotomayor is our first member from Ohio State University and we have 10 new members from the University of Chicago: Erin Adams, Demet Arac-Ozkan, Sean Crosson, Allan Drummond, Bob Keenan, Shohei Koide, Joe Piccirilli, Phoebe Rice, Ron Rock, and Tobin Sosnick Welcome to our new members!
Software Update
We have a small software update for this month, including Geneious 7.0.5, LigPlus 1.45, CCP4 updates 03-05, new OpenBabel python bindings and PyMOL 1.7b3. The PyMOL beta is a non-default version, so you'll have to use a version override to enable it.
We have also included recent nightly versions of Phenix and Rosetta configured for the Phenix-Rosetta refinement process. By configuring the "nightly" version for both applications, the phenix.rosetta_refine command becomes available.
Publications
Since our last newsletter, the following publications have appeared from Consortium member labs:
- Beese Lab, DukeU Medical Ceter: Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design.
- Boggon Lab, YaleU School of Medicine:
- Signaling pathways and the cerebral cavernous malformations proteins: lessons from structural biology.
- Identification of PLX4032-Resistance Mechanisms and Implications for Novel RAF Inhibitors.
- Bradner Lab, Dana-Farber Cancer Institute: BET-bromodomain inhibition of MYC-amplified Medulloblastoma.
- Chazin Lab, VanderbiltU: Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach.
- Crane Lab, CornellU: Flavin reduction activates Drosophila cryptochrome.
- Darst Lab, RockefellerU: Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1.
- Fan Lab, ColumbiaU: Structural mechanism of ligand activation in human GABAB receptor.
- Garcia Lab, StanfordU: Activation and allosteric modulation of a muscarinic acetylcholine receptor.
- Hogle Lab, Harvard Medical School: Cryo-electron microscopy reconstruction shows poliovirus 135S particles poised for membrane interaction and RNA release.
- Kahne Lab, Harvard University: Lipoprotein Activators Stimulate Escherichia coli Penicillin-Binding Proteins by Different Mechanisms.
- Lemmon Lab, UPenn School of Medicine: Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions.
- Lindsley Lab, VanderbiltU: Phospholipase D2 mediates survival signaling through direct regulation of Akt in glioblastoma cells.
- Marnett Lab, VanderbiltU: Replication, Repair, and Translesion Polymerase Bypass of N(6)-Oxopropenyl-2'-deoxyadenosine.
- Meiler Lab, VanderbiltU: Multiple mechanisms determine ER network morphology during the cell cycle in Xenopus egg extracts.
- Miller Lab, Mass General Hospital: Human α1β3γ2L Gamma-Aminobutyric Acid Type A Receptors: High-Level Production and Purification in a Functional State.
- Niessing Lab, Helmholtz Zentrum Muenchen: Role of Loc1p in assembly and reorganization of nuclear ASH1 messenger ribonucleoprotein particles in yeast.
- Rapoport Lab, Harvard Medical School: Multiple mechanisms determine ER network morphology during the cell cycle in Xenopus egg extracts.
- Roll-Mecak Lab, NINDS-NIH: Botany. Shining light at microtubule crossroads.
- Southworth Lab, UMichigan: The Molecular Chaperone Hsp70 Activates Protein Phosphatase 5 (PP5) By Binding the Tetratricopeptide Repeat (TPR) Domain.
- Skiniotis Lab, UMichigan: Characterization of a Highly Flexible Self-Assembling Protein System Designed to Form Nano Cages.
- Walensky Lab, Dana-Farber Cancer Institute: A phospho-BAD BH3 helix activates glucokinase by a mechanism distinct from that of allosteric activators.
- Walker Lab, Harvard Medical School:
- HCF-1 is cleaved in the active site of O-GlcNAc transferase.
- Moenomycin Resistance Mutations in Staphylococcus aureus Reduce Peptidoglycan Chain Length and Cause Aberrant Cell Division.
- Lipoprotein Activators Stimulate Escherichia coli Penicillin-Binding Proteins by Different Mechanisms.
- Walz Lab, Harvard Medical School: The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway.
- Yudin Lab, UToronto: Exocyclic Control of Turn Induction in Macrocyclic Peptide Scaffolds.
- Zhou Lab, Baylor College of Medicine: Structural basis of the alternating-access mechanism in a bile acid transporter.
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.