Dear Consortium Members and Affiliates,
As the first month of 2016 comes to an end we have news for you on several fronts, including a date to save for our workshop on Structure Determination Techniques, the latest from our software webinar series, plans for the next SBGrid-Schrodinger Working Group, a software push with 15 updates and 3 new applications, two new members to welcome, two new SBGrid citations, and highlights from four member publications.
Please Save the Date for an SBGrid Workshop focused on Structure Determination Techniques - May 23-24, 2016. Our lineup of speakers will include Kay Diederichs, Paul Emsley, Wayne Hendrickson, James Holton, Piotr Sliz, and Graeme Winter. We will announce program details and open registration in the coming weeks.
In webinar news, we got some pointers from Roberto Tejero (despite his blossoming cold) on his software PDBStat on Tuesday. You'll find a recording of his webinar posted on YouTube. During the next few months we have a series of webinars scheduled that focuses on applications included in the CCP4 Suite. Be sure to join us to hear from:
- James Foadi on BLEND - February 9th
- Raj Pannu on CRANK2 - March 8th
- Daniel Rigden on AMPLE - April 12th
We had our first SBGrid-Schrodinger Working Group for the new year a couple of weeks ago, and heard again from Woody Sherman, this time on the role of water molecules in protein preparation. In our next couple of meetings we'll hear first about Schrodinger's Protein Preparation Wizard and then on Free Energy Perturbation. Dates and details will be announced soon.
Our January software update includes new versions of 3DNA, ALBULA, ARCIMBOLDO_LITE, ATSAS, CCP4, CTFFIND4, EPMR, Frealign, FRODOCK, Geneious, HKL2000, IMOD, Phenix, Phenix/DivCon, and Rosetta, along with three new applications: FindDQE, mag_distortion_estimate and correct, and SASSIE.
To kick off 2016, two new members, representing institutions that are also new to SBGrid, have joined: Graeme Winter from Diamond Light Source and Nozomi Ando from Princeton University. Welcome to our newest members!
For the month of January, SBGrid received 2 new citations in member publications, one in Science from Thomas Schwartz's MIT laboratory Science. 2016. 6268: 53-58, and another in the Journal of Medicinal Chemistry that included SBGrid members Emil Pai of U Toronto and Suzanne Walker of Harvard Medical School. J. Med. Chem., 2016, 59 (2), pp 624–646.
Over 53 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- After a flurry of new structures determined for MFS transporters, Pär Nordlund's group at Nanyang Technological University in Singapore have published a review of these proteins, to examine how this new data expands our understanding of the conformational cycle of MFS transporters. Nature Rev Mol Cell Biol. 17:123-132.
- From SBGrid members Jue Chen and Thomas Walz at Rockefeller University, comes an article in Nature that shows the structure of TAP in complex with its HSV-1 inhibitor ICP47, offering new insight into how some viruses inhibit TAP activity. Nature.529:537-540.
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight two articles this month. The first appeared in Nature from James Bradner's group at Dana-Farber Cancer Institute, and gives us a new understanding of BET bromodomain inhibition in Triple-negative breast cancer. Read Kristen's summary here. Also on her radar was another story appearing in Nature from Peter Kwong's NIH laboratory in which he examined broadly neutralizing antibodies against HIV-1 from multiple donors in an effort to identify patterns of development. Read more on Tumblr.
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data along with the PDB record and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
3DNA version 2.3 includes a new experimental section of ‘simple’ base-pair and step parameters for a more ‘intuitive’ description of structures with non-Waton-Crick pairs.
ALBULA version 3.2 makes it possible to directly read bit-shuffle LZ4-compressed data.
ARCIMBOLDO_LITE version 4.0.0 is now available for Linux.
ATSAS version 2.7.1-1 includes improved handling of zero intensities and dummy residues in crysol, data range selection in all dattools, reduced memory footprint in datmerge, and general performance improvements in a number of programs.
CCP4 version 7.0 is now in the SBGrid tree. This release is a big one for CCP4, including a new graphical interface, the addition of SHELX, DIALS, and ARCIMBOLDO, and updates to many of the other component programs.
CTFFIND4 version 4.0.17 was pushed out for Mac and Linux.
EPMR version 16.01 is the new default.
FindDQE version 150706 was just added to the SBGrid collection. FindDQE, from Nikolaus Grigorieff's group, determines the detective quantum efficiency (DQE) of a detector.
Frealign version 9.11 is available for Linux and this update includes asymmetric reconstructions, which can be enabled using lowercase symmetry symbols.
FRODOCK version 2.0 was significantly improved with the addition of a complementary knowledge-based protein-protein potential.
Geneious version 9.0.5 is primarily a bug fix release.
HKL2000 version 710 corrects the ADSC pad HF-4M and Dectris Eiger 16M formats, the blind region input for non-zero 2theta data sets, the anomalous mean I/sigma value reported by the scaling report, and the list of loaded data sets.
IMOD version 4.7.15 includes an improvement in eTomo when setting InvertYLimits in corrsearch3d, fixes Corrsearch3d so that Z slice limits picked in etomo will specify the proper Y range in the unrotated volume, updates Batchruntomo to apply directives for options in golderaser.com and to scale fine alignment shifts by the prealign binning when combining with the prealign shifts, and modifies Ccderaser to take mean inside instead of outside boundary contours.
mag_distortion_estimate and correct version 1.0 is also new to SBGrid. This application is another from the Grigorieff lab, for use when estimating magnification distortions in electron micrographs using images of polycrystalline samples such as gold shadowed diffraction gratings.
Phenix nightly build dev-2276 is now available via version override.
Phenix/DivCon was upgraded to version b3072(Linux)/b3111(Mac).
Rosetta was updated to version 2016.02.58402.
SASSIE was just added to the SBGrid Suite. This program suite is used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data. There are two versions of SASSIE, one that is open source that excludes the "courtesy modules", and another that is available to non-profit members after registration that includes “courtesy modules,”(NAMD, Cryson, Crysol, and Hydropro).
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.