Dear Consortium Members and Affiliates,
February is a wrap as we send you news from the SBGrid front. Read on for a final plug for our Ambassador program, webinars you can watch and plan to attend, a profile on SBGrid PI Brandt Eichman, a spring seminar series from Schrödinger, 7 software updates and 2 new applications, one new member to welcome, and 3 publication highlights to share.
Last call for those who wish to participate in the SBGrid Ambassador Program. If you'd like to represent your fellow laboratory, departmental, or institutional scientists in helping us identify computing challenges and address unmet needs of the community, you can apply to join in this national forum to help steer the development of SBGrid. Read the full details and contact Michelle by Friday to apply.
We were happy to see so many of you online for the OpenMM webinar with Peter Eastman today. We’ll have that video available soon, but in the meantime our January webinars, featuring xfel tools cctbx.xfel, Iota, and Prime, are all posted online at SBGridTV. We’ll next hear from NE-CAT Assistant Director Frank Murphy on RAPD, a package for automated autoindexing, integration, and structure solution of macromolecular crystallographic date. Join us March 21st.
We caught up with Brandt Eichman of Vanderbilt University for our February member tale. Eichman described the circular nature of his own scientific research, which began in graduate school trying to untangle the four-stranded knots of Holliday junctions and continues with a similar knot found when examining motor protein DNA repair work. Read more about Eichman’s work on DNA damage and repair in our February webtale.
Schrödinger has announced a new spring seminar series. The first, which was held today, focused on Lead Optimization with FEP+. The next two will focus on What's new in Maestro 11 and Ligand-based Drug Design using Phase. Find out more.
Our February software release includes updates to 3DNA, ATSAS, BLAST+, CCP4, cython, DIALS, DSSR EMAN2, EPMR, GROMACS ImageJ, MAFFT, MotionCor2, NAMD, Relion, Schrödinger, Spider, XDrawChem, and XRayView. Two new applications were also added to the collection: eiger2cbf and NMRFAM-Sparky
We had one new member join this month: Daryl Klein from Yale School of Medicine. Welcome to our newest member!
Member Publications
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the Structural Biology Data Grid along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid received one new citation during the last month, this one from our own Piotr Sliz at Harvard Medical School [Abstract]
Over 80 publications from SBGrid member laboratories appeared in our February search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- James Berger's group at Johns Hopkins University School of Medicine found that DNA replication initiation in the bacterial, archaeal, and eukaryotic domains have evolved in surprisingly different ways. Read more in Science. [Abstract]
- In an article appearing in Cold Spring Harbor Perspectives in Biology, Peter Kwong of the NIH offers a structural biologist's view on drug design and describes how atomic-level information provides a new options for developing vaccines for viruses that have resisted standard approaches. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper in the journal Structure, from Oliver Ernst's lab at the University of Toronto, that describes a new method of crystallization for use with membrane proteins that are vulnerable to detergents. [More on Tumblr].
Software Changes
3DNA was updated to version 2.3-20170208
ATSAS is now at version 2.8.0-2. This version supports Ubuntu 16.04, Debian 8 and includes many improvements to libsaxsdocument. Several new programs have been added, including secplot to plot and process SEC-SAXS data, sasre, which estimates resolution for ab initio model ensemble, seqstat to get statistics about a protein from its amino acid sequence, pdbstat to statistics about a protein in a PDB file, databsolute for normalizing a SAXS curve to an absolute intensity scale, adderrors for adding simulated experimental errors to a dataset, and partistr to divide protein coordinates (PDB) into subdomains according to dynamics (NMA).
BLAST+ was bumped to version 2.6.0. This update improves support for accession.version as the primary identifier and the speed of blastdbcmd when dumping information from a database.
CCP4 version 7.0.028 includes updates to DIALS and XIA2 along with some other bug fixes.
The Python module, Cython, was update to version 0.25.2.
DIALS is now at version 1.4.3.
DSSR version 1.6.5 includes revised detection of pairs and helices/stems, allows analysis of user base pair customization, adds an analysis of the global curvature for each nucleic acid chain.
eiger2cbf v160530 is new to SBGrid. This simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format. Find out more.
EMAN nightly release 2 2.2_rel_20170126 was added. This version is available by version override. The current default version is still 2.1.2
EPMR was updated to version 16.07.1.
Gromacs version 5.1.4 is a general bug fix and performance improvement release.
MAFFT is now at version 7.30. Since our last update the developers have introduced several new experimental options and have wiped out a number of bugs.
MotionCor2 version 20170130 was pushed out.
NAMD version 2.12b1 was added. This update has many advantages over its predecessor including GPU-accelerated simulations, improvements to vectorization and new kernels for Xeon Phi Knight's Landing and scaling for large implicit solvent simulations and multi-threaded "smp” builds, and many other performance improvements.
NMRFAM-Sparky is new to SBGrid. At version 201701, NMRFAM-Sparky is a new version of Sparky renamed because NMRFAM has taken over the original Sparky to support advances in the biomolecular NMR field. Tom Ferrin and Tom Goddard of UCSF have generously allowed NMRFAM to develop the original Sparky, which remains the most popular NMR biomolecular analysis tool available.
Relion version 2.0.3 is now a stable release and the new default. This version will allow GPU use for the most demanding calculations (relion_refine and relion_autopick), has a new GUI, to allow on-the-fly image processing during data acquisition, and introduces functionality to process helical assemblies.
Schrodinger's latest update 2017-1 includes several improvements to the Maestro interface, Quicker and more robust relaxation protocol for membrane bound proteins and a number of updates to PLDB including a revamped interface.
Spider is at version 24.01. You’ll notice new protocols for use with PBS queuing, for aligning direct electron capture image frames, and for refinement without defocus groups with ‘Gold standard’ workflow, Also new is an option for spherical deconvolution of reconstructed volumes and allowance for longer file names.
XdrawChem was updated to version 1.10.2 and is now available for Mac users.
XRayView version 5.0 was pushed out.
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.