Dear Consortium Members and Affiliates,
We're sending a short December update a bit early, before the holiday whirlwind sweeps everyone away. We have news about the science happening in Qing Fan's lab at Columbia University, a reminder to check out SBGrid's YouTube channel and our growing library of software webinars, and a software release including 8 updates and 1 new software application.
SBGrid staff will be on holiday from December 24th through January 2nd. During the break we'll tend to emergencies, but the small stuff will be on hold. Best wishes to all in the New Year!
In this month's webtale, we looked in on Qing Fan, assistant professor at Columbia University. She talked with us about the GABAB structure she solved and reported on in PNAS earlier this year, and how her work still focuses on understanding the basic mechanisms at play, even while collaborating with others to screen for drugs with therapeutic potential.
We still receive emails from members who only just discovered the SBGrid YouTube channel. We've amassed a nice collection of software tutorials by now, with our monthly webinars and the presentations from our 2014 computing school. If you haven't done so yet, please take a moment to peruse library and be sure to subscribe to receive announcements when new videos are added.
Our December software update is scheduled for release before the end of the month and will include updates to ATSAS, CCP4, CcpNmr, Coot, DynDom, PyMOL, relax, and xia2 as well as one new software application: Clustal Omega.
Software Changes
ATSAS is now at version 2.6. This version includes a number of new features and bug fixes, which are detailed here. Note, inclusion of ATSAS software in your installation requires registration with the developer. See our ATSAS software page for additional instructions.
CCP4 was updated to include patch 22.
CcpNmr is now at version 2.4.1.
Clustal Omega is new to the SBGrid collection. Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
Coot has been updated to version 0.8.0-3 for Mac and 0.8.1-5441 for LInux. This release includes Pubchem drag and drop support, new glyo and ProSMART modules, and an option to run python commands from the command line. There are a number of other new features and fixes described in the release notes.
DynDom is now at version 1.5. No additional information is available.
PyMOL was updated to version 1.7.4, a release that focuses on adding or improving support for mmCIF and several other file formats.
relax version 3.3.4 is a major feature and bug fix release. It adds support for saturation and inversion recovery R1 experiments and fixes a bug for storing multi-dimensional numpy data structures as IEEE 754 byte arrays.
xia2 3.8.0 was pushed out. With this update xia2 includes support for DIALS software, kills a number of nasty bugs, and replaces Scala in all pipelines with Aimless.
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.
- Rick Cerione's Group, Cornell U: Simultaneously Targeting Tissue Transglutaminase and Kidney Type Glutaminase Sensitizes Cancer Cells to Acid Toxicity and Offers New Opportunities for Therapeutic Intervention.
- Allan Drummond's Group, U Chicago:
- Christopher Garcia's Group, Stanford U: Insights Into Cytokine-Receptor Interactions from Cytokine Engineering.
- Joseph Schlessinger's Group, Yale U: Whole-exome sequencing characterizes the landscape of somatic mutations and copy number alterations in adrenocortical carcinoma.
- James Hurley's Group, U California, Berkeley: Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex.
- Steve Harrison's Group, Harvard Medical School:
- Veritas per stucturam.
- Sequential conformational rearrangements in flavivirus membrane fusion.
- Michael Sattler's Group, Institute of Structural Biology: Breaking the protein-RNA recognition code.
- Jamie Cate's Group, U California, Berkeley: Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase.
- James Bradner's Group, Dana-Farber Cancer Institute:
- Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor.
- AF10 Regulates Progressive H3K79 Methylation and HOX Gene Expression in Diverse AML Subtypes.
- Andrei Yudin's Group, U Toronto: Boron-Containing Enamine and Enamide Linchpins in the Synthesis of Nitrogen Heterocycles.
- Catherine Drennan's Group, MIT: SPASM and Twitch Domains in AdoMet Radical Enzyme Structures.
- Christopher Ackerson's Group, Colorado State U: Oxidative decomposition of Au25(SR)18 clusters in a catalytic context.
- Tom Ellenberger's Group, Washington U School of Medicine: A Quantitative Assay Reveals Ligand Specificity of the DNA scaffold repair protein XRCC1 and Efficient Disassembly of Complexes of XRCC1 and the Poly (ADP-ribose) polymerase 1 by PAR glycohydrolase.
- Roderick MacKinnon's Group, Rockefeller U: Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
- Dinshaw Patel's Group, Memorial Sloan Kettering Cancer Center:
- Uridylation by TUT4 and TUT7 Marks mRNA for Degradation.
- Adenylation of Maternally Inherited MicroRNAs by Wispy.
- Tim Springer's Group, Boston Children's Hospital: Metal ion and ligand binding of integrin α5β1.
- Tina Iverson's Group, Vanderbilt U: Arrestin Expression in E. coli and Purification.
- Wes Sundquist's Group, U Utah: Putting a finger in the ring.
- Keith Miller's Group, Massachusetts General Hospital: Dodecyl maltopyranoside enabled purification of active human GABA type A receptors for deep and direct proteomic sequencing.
- Georgios Skiniotis's Group, U Michigan: Molecular Basis for DPY-30 Association to COMPASS-like and NURF Complexes.
- John Williams's Group, City of Hope: Internal Dynamics of Dynactin's CAP-Gly is Regulated by Microtubules and Plus End Tracking Protein EB1.
- Filippo Mancia's Group, Columbia U: Structure of a mammalian ryanodine receptor.
- James Fraser's Group, U California, San Francisco: Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.
- Frank Sicheri's Group, U Toronto: Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation.
- David Wilson's Group, La Trobe U: A 2,2'-bipyridine coordination complex of [ICl2](+)
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.