Dear Consortium Members and Affiliates,
As April comes to a close and spring fever starts to set in, we have a brief update from the SBGrid front, with our newest webinar available online, one to watch live next week, a monthly SBGrid tale featuring Alexandre Bonvin of HADDOCK fame, three member publication highlights, and a software release that includes six updates and two new titles.
Join us next week for a webinar from Thorsten Wagner and an introduction to crYOLO, automated particle picking software. Details here. You can also catch last month's webinar on TomoAlign, with José-Jesús Fernéndez, on our YouTube channel. Watch Here.
Our April developer tale took us to The Netherlands, as we connected with Alexandre Bonvin at the Bijvoet Center, Utrecht University. Bonvin sets us straight about the origins of HADDOCK (no fish are involved!) and gives us some background on the CAPRI competition, which relies on structural biologists to provide coordinates of unpublished structures for computational biologists to test their algorithms in blind predictions. Read the full story.
We have 8 software updates that are going out for April. Watch for new versions of adxv, CCP4, Gromacs, OpenMM, pdb-tools, and R, and two new software titles: AWS CLI and py4xs.
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 SBGrid Data Bank 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.
In April, SBGrid's eLife paper received 3 new citations from SBGrid-member laboratories, including those from Melanie Ohi of the University of Michigan in the Journal of Molecular Biology [Abstract]; Columbia University's Qing Fang, in PNAS [Abstract], and Karen Anderson at the Yale University School of Medicine, in the Journal of Antiviral Research. [Abstract].
Over 70 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple notable highlights below:
- A review in Protein Science, by the NIH's Adrian Ferré‐D'Amaré, addresses the rising need for new and more effective tools for visualizing RNA in cells. Ferré‐D'Amaré discusses how fluorogenic RNA‐fluorophore complexes have emerged as an attractive and more ideal tool for RNA visualization. [Abstract]
- In the Journal of Molecular Biology, Melanie Ohi of the University of Michigan has a new publication in which the authors determined the structures of VacA oligomers and, in so doing, helped to advance our knowledge of how VacA oligomerizes when Helicobacter pylori colonizes the human host. [Abstract]
- From our graduate student desk: Harvard student Kristen Rodrigues highlighted a publication from the laboratories of Dierk Niessing and Michael Sattler that appeared in Nature Communications in which the authors investigate the molecular basis of RNA-binding by Staufen proteins and reveal the previously under-appreciated importance of Drosophila Stau RNA binding domains 1 & 2. [More on Tumblr]
adxv was bumped to version 1.9.14.
AWS CLI is new to SBGrid at version 1.16.140. AWS CLI is a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
CCP4 is now at version 7.0.073, with an update to molrep that includes improvements to the multi_copy_search function and a new keyword in RMV; lorestr integration with CCP4 Cloud, a crank2 bug fix, improvements to sftools, and updates to coot and WinCoot.
GROMACS was bumped to version 2019.1. With the 2019 release you'll notice improved performance with simulations, which now automatically run using update groups of atoms whose coordinate updates only have intra-group dependencies; new support for Intel integrated GPUs with OpenCL, for offloading non-bonded interactions; and a new option for PME long-ranged interactions to run on a single AMD GPU using OpenCL.
OpenMM is now at version 7.3.0, with many new updates and improvements, including a new force class called RMSDForce, which computes the RMSD between the current positions and a reference structure over a set of particles; a new option to allow vector functions, such as cross products and dot products, in CustomIntegrator expressions; support for the polarizable force field in the CHARMM importer and a larger set of features (functional forms, combination rules, virtual site types, etc.) in the Gromacs importer; and a new feature in NonbondedForce to define global parameters, then automatically modify the charges and LJ parameters of particles based on them.
pdb-tools was updated to version 2.0.0 is an overhaul of the original pdb-tools collection to unify the user-interface across all scripts as well as the internals of the code. Some scripts are not backwards compatible.
py4xs was just added to SBGrid. py4xs is a python package for processing x-ray scattering data, first developed at the X9 beamline at NSLS, but revised multiple times and now in use at the LiX beamline at NSLS-II.
R is now at version 3.5.1.
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.